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had trouble with their installation. It's not clear if some of the packages are still being actively developed and supported. -The one I recommend, since I have successfully used it with LAMMPS, is -Pypar. Pypar requires the ubiquitous "Numpy -package"_http://numpy.scipy.org be installed in your Python. After -launching python, type +The packages Pypar and mpi4py have both been successfully tested with +LAMMPS. Both are widely used. Pypar is simpler and easy to set up +and use, but supports only a subset of MPI. Mpi4py is more +MPI-feature complete, but also a bit more complex to use. As of +version 2.0.0, mpi4py is the only python MPI wrapper that allows +passing a custom MPI communicator to the LAMMPS constructor, which +means one can easily run one or more LAMMPS instances on subsets of +the total MPI ranks. + +:line + +Pypar requires the ubiquitous "Numpy package"_http://numpy.scipy.org +be installed in your Python. After launching Python, type import numpy :pre @@ -361,6 +370,51 @@ the right one. :line +To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it +and from its main directory, type + +python setup.py build +sudo python setup.py install :pre + +Again, the "sudo" is only needed if required to copy mpi4py files into +your Python distribution's site-packages directory. To install with +user privilege into the user local directory type + +python setup.py install --user + +If you have successully installed mpi4py, you should be able to run +Python and type + +from mpi4py import MPI :pre + +without error. You should also be able to run python in parallel +on a simple test script + +% mpirun -np 4 python test.py :pre + +where test.py contains the lines + +from mpi4py import MPI +comm = MPI.COMM_WORLD +print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre + +and see one line of output for each processor you run on. + +IMPORTANT NOTE: To use mpi4py and LAMMPS in parallel from Python, you +must insure both are using the same version of MPI. If you only have +one MPI installed on your system, this is not an issue, but it can be +if you have multiple MPIs. Your LAMMPS build is explicit about which +MPI it is using, since you specify the details in your lo-level +src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find +information about the MPI it uses to build against. And it tries to +load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find +the MPI library that LAMMPS is using. If you have problems running +both mpi4py and LAMMPS together, this is an issue you may need to +address, e.g. by moving other MPI installations so that mpi4py finds +the right one. + +:line + 11.6 Testing the Python-LAMMPS interface :link(py_6),h4 To test if LAMMPS is callable from Python, launch Python interactively @@ -491,10 +545,11 @@ correspond one-to-one with calls you can make to the LAMMPS library from a C++ or C or Fortran program. lmp = lammps() # create a LAMMPS object using the default liblammps.so library -lmp = lammps(ptr=lmpptr) # ditto, but use lmpptr as previously created LAMMPS object -lmp = lammps("g++") # create a LAMMPS object using the liblammps_g++.so library -lmp = lammps("",list) # ditto, with command-line args, e.g. list = \["-echo","screen"\] -lmp = lammps("g++",list) :pre + 4 optional args are allowed: name, cmdargs, ptr, comm +lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object +lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator. Requires mpi4py 2.0.0 or later +lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library +lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre lmp.close() # destroy a LAMMPS object :pre diff --git a/doc/doc2/Eqs/.log b/doc/doc2/Eqs/.log deleted file mode 100644 index 39ba97a0d2..0000000000 --- a/doc/doc2/Eqs/.log +++ /dev/null @@ -1,30 +0,0 @@ -This is TeX, Version 3.14159 (Web2C 7.4.5) (format=latex 2008.11.14) 27 AUG 2011 15:16 -**pair_sph_tait -(/usr/share/texmf/tex/latex/tools/.tex -LaTeX2e <2001/06/01> -Babel and hyphenation patterns for american, french, german, ngerman, n -ohyphenation, loaded. -File ignored) -* -(Please type a command or say `\end') -*x - -! 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--git a/doc/doc2/Eqs/compute_fep_vol.tex b/doc/doc2/Eqs/compute_fep_vol.tex deleted file mode 100644 index 0301e39788..0000000000 --- a/doc/doc2/Eqs/compute_fep_vol.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( - - \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right) -\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \] - -\end{document} diff --git a/doc/doc2/Eqs/compute_gyration.jpg b/doc/doc2/Eqs/compute_gyration.jpg deleted file mode 100644 index 228544443459e2c13b9ba1e860d8abd5e02f9ffb..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3658 zcmZ{nc{J3G_s2hD-?EIYjGe&@Lm_0zG75uaY%$0Z5i>FvvddnCF~}oJnn8BTmIswY zR3`gal0n&@vP)0%^*z7e_n+^1zW1JU|GD?P?)~GQbMKom#rOj7qb^%q20$PXV1D8N zV+KG1tjsJdEX=GYft8h&jh%;s{lxgVxjA_R_`qNRJ^=wi5phvLAu(YAfzvXl#Uv!8 zq@)BzW#wfh<;5kXBpELOZVtc+qy_>B0E{<)H~<2ePgpWlpshOL$r!n-KDz 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\cos (2\phi) + D_3 \cos (3\phi) ] + \\ - & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\ - E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\ - E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3) -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg b/doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg deleted file mode 100644 index ea0a7550f8a0f90a9f8cecd564571cb3cee7aa42..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8004 zcmd6McQ71K)bENOmLN*lMG%q*qL;N&L~n_Nu!t6Q)mrjG?flN=)a4T3hNh~9Du9fP44{5h z0GG1>WdJ2P1qB5;!= zFb@w83p<|xAGZLAn}_?d4M0Z&FuOKLM#coV>;!-SWPoer|1rmZf|81yg8CX6&6QU9 z27ru$jQrY_;7Uq+)#X2WQ&3VdF;m}W5r1-%?}a4|yTohvq!Cs&{-^o|h@jy3F}aV! z%7)gSAqk1eRhKgWn*SL55#S;@;=doc$oI(@NwJsoJx+^1W+V5zH1l9@ca1AN%0!W{ z?rShvcdi7$+~KP?C4b~3vaU51d1UqVX9!Nb>d?k(8M@l1yT1`4+it3!@3Wo?n!8cj 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e6813b125c..0000000000 --- a/doc/doc2/Eqs/eff_Ne.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E_{Ne} = - \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i,j} {\frac{{Z_i }}{{R_{ij} }}Erf\left( {\frac{{\sqrt 2 R_{ij} }}{{s_j }}} \right)} -$$ - -\end{document} diff --git a/doc/doc2/Eqs/eff_Pauli.jpg b/doc/doc2/Eqs/eff_Pauli.jpg deleted file mode 100644 index 61bb8652e390a0970aed8727753dd6a248ec9733..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5676 zcmb`LcT5xPx5tZR3J3_YDM%SAONQ(zQmCj1$X-HOQYe&4%djG{w}LXtQig?>J<60N zOQ0ZowG5e}Yy@N!u5W%fH@Sb_M2!M);3SjUz z02d^HE`SC|O-&7?`FqgN(9qH`(bN5fg^`hgiH+szRW=qjHg-;aE_M#yYiw-X*SUEG z1Ox>I*|~&8gh3+wAVJVY8-S4>U`>@vMa2fV=mhWsr~sFM|7!dXG_*i!x=Zv_f3x>l z0aVmfz)RGBRp~D?{w?{pnwo}|?JC`Mc41i^4r51pIb_H+PVilM6Ti3bD{Dr%L_`&p zp7^GG95FSwaDus@U%zYrelY`}|5rl`a4N<2{|xH0n@QR7K}(Rq&~SiC6}Oo7>ENHn zFNzE}JJ$J}IVtMR4USCSez5_En9=EnJnuh{GhA=a$+t@~KlhZ8!qBB&(%vMsE}M1z 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b/doc/doc2/Eqs/fix_gld1.tex deleted file mode 100644 index baa0f32a5b..0000000000 --- a/doc/doc2/Eqs/fix_gld1.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\usepackage{amsmath} - -\begin{document} - -\begin{align*} - &{\bf F}_{j}(t) = {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\ - &\Gamma_j(t-s) = \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ - &\langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = \text{k$_\text{B}$T} ~\Gamma_j(t-s) -\end{align*} - -\end{document} diff --git a/doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg b/doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg deleted file mode 100644 index 9d82b40ecb009745f6b984f5092b42008a057380..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4643 zcma)=S2P@q5`cI0|JOUKEYXrE(M6YR5Ftb)h#spiR$Vp9PXw`QtWFXox_@;NEz7PJ zK?G~{vP#s|`_2Dy&%F=#ocql=^Dr}K%ELU&Tu)xl1DGD^=;;7}Kp^1ZZvk8r01yBr 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a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex b/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex deleted file mode 100755 index 41ca4674e9..0000000000 --- a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex +++ /dev/null @@ -1,16 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\partial_t \rho + \partial_{\beta}\left(\rho u_{\beta}\right)= 0 -$$ -$$ -\partial_t\left(\rho u_{\alpha}\right) + \partial_{\beta}\left(\rho u_{\alpha} u_{\beta}\right) = \partial_{\beta}\sigma_{\alpha \beta} + F_{\alpha} + \partial_{\beta}\left(\eta_{\alpha \beta \gamma \nu}\partial_{\gamma} u_{\nu}\right) -$$ - -\end{document} - - - - diff --git a/doc/doc2/Eqs/fix_lb_fluid_properties.jpg b/doc/doc2/Eqs/fix_lb_fluid_properties.jpg deleted file mode 100644 index 3d70cd7667461b8f4f8c96c5d271ad2662e88bb5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3471 zcmaKuc{J4f8^^!XShF=`ow1HCS+YjRQe5&&wp-E+Zpjvvn6Wjo7L{S{SVy)jL#n}8 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    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    - -

    LAMMPS Documentation -

    -

    10 Aug 2015 version -

    -

    Version info: -

    -

    The LAMMPS "version" is the date when it was released, such as 1 May -2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of -the WWW site. Each dated copy of LAMMPS contains all the -features and bug-fixes up to and including that version date. The -version date is printed to the screen and logfile every time you run -LAMMPS. It is also in the file src/version.h and in the LAMMPS -directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). -

    -
    • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS. - -
    • If you browse the HTML doc pages included in your tarball, they -describe the version you have. - -
    • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. - -
    • There is also a Developer.pdf file in the doc -directory, which describes the internal structure and algorithms of -LAMMPS. -
    -

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. -

    -

    LAMMPS is a classical molecular dynamics simulation code designed to -run efficiently on parallel computers. It was developed at Sandia -National Laboratories, a US Department of Energy facility, with -funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). -

    -

    The primary developers of LAMMPS are Steve Plimpton, Aidan -Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses. -

    - - - - -
    - -

    The LAMMPS documentation is organized into the following sections. If -you find errors or omissions in this manual or have suggestions for -useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. -

    -

    Once you are familiar with LAMMPS, you may want to bookmark this -page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. -

    -

    PDF file of the entire manual, generated by -htmldoc -

    -

    -

    -
    1. -Introduction - - -
    2. Getting started - - -
    3. Commands - - -
    4. Packages - - -
    5. Accelerating LAMMPS performance - - -
    6. How-to discussions - - -
    7. Example problems - -
    8. Performance & scalability - -
    9. Additional tools - -
    10. Modifying & extending LAMMPS - - -
    11. Python interface - - -
    12. Errors - - -
    13. Future and history - - - -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html deleted file mode 100644 index 7a99a28735..0000000000 --- a/doc/doc2/Manual.html.html +++ /dev/null @@ -1,318 +0,0 @@ - - - - -LAMMPS Users Manual - - - - - - - - - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - -
    - -

    - -

    LAMMPS Documentation -

    -

    20 Nov 2015 version -

    -

    Version info: -

    -

    The LAMMPS "version" is the date when it was released, such as 1 May -2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of -the WWW site. Each dated copy of LAMMPS contains all the -features and bug-fixes up to and including that version date. The -version date is printed to the screen and logfile every time you run -LAMMPS. It is also in the file src/version.h and in the LAMMPS -directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). -

    -
    • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS. -

      -

    • If you browse the HTML doc pages included in your tarball, they -describe the version you have. -

      -

    • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. -

      -
    • There is also a Developer.pdf file in the doc -directory, which describes the internal structure and algorithms of -LAMMPS. -
    -

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. -

    -

    LAMMPS is a classical molecular dynamics simulation code designed to -run efficiently on parallel computers. It was developed at Sandia -National Laboratories, a US Department of Energy facility, with -funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). -

    -

    The primary developers of LAMMPS are Steve Plimpton, Aidan -Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses. -

    - -
    - -

    The LAMMPS documentation is organized into the following sections. If -you find errors or omissions in this manual or have suggestions for -useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. -

    -

    Once you are familiar with LAMMPS, you may want to bookmark this -page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. -

    -

    PDF file of the entire manual, generated by -htmldoc -

    -

    -

    -
    1. -Introduction - - -
    2. Getting started - - -
    3. Commands - - -
    4. Packages - - -
    5. Accelerating LAMMPS performance - - -
    6. How-to discussions - - -
    7. Example problems - -
    8. Performance & scalability - -
    9. Additional tools - -
    10. Modifying & extending LAMMPS - - -
    11. Python interface - - -
    12. Errors - - -
    13. Future and history - - - -
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zm^pbNznu>X;`z2tiBT}xEjfpMbkC=V^MGT-VAOeMe#UWf=P)@{873YxviF5FXa*9L6#Gn$~ l;@n(9fd6|JU4W1fmV={#z2hJ856a1jpsuE)6IYPH`aeXaRMh|g diff --git a/doc/doc2/PDF/pair_resquared_extra.tex b/doc/doc2/PDF/pair_resquared_extra.tex deleted file mode 100644 index 945ee562d7..0000000000 --- a/doc/doc2/PDF/pair_resquared_extra.tex +++ /dev/null @@ -1,113 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{center} - -\large{Additional documentation for the RE-squared ellipsoidal potential \\ - as implemented in LAMMPS} - -\end{center} - -\centerline{Mike Brown, Sandia National Labs, October 2007} - -\vspace{0.3in} - -Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be -given by the ellipsoid radii. Let the relative energy matrices -$\mathbf{E}_i = \mbox{diag} (\epsilon_{ia}, \epsilon_{ib}, -\epsilon_{ic})$ be given by the relative well depths -(dimensionless energy scales inversely proportional to the well-depths -of the respective orthogonal configurations of the interacting molecules). -Let $\mathbf{A}_1$ and $\mathbf{A}_2$ be the transformation matrices -from the simulation box frame to the body frame and $\mathbf{r}$ -be the center to center vector between the particles. Let $A_{12}$ be -the Hamaker constant for the interaction given in LJ units by -$A_{12}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2$. - -\vspace{0.3in} - -The RE-squared anisotropic interaction between pairs of -ellipsoidal particles is given by - -$$ U=U_A+U_R, $$ - -$$ U_\alpha=\frac{A_{12}}{m_\alpha}(\frac\sigma{h})^{n_\alpha} -(1+o_\alpha\eta\chi\frac\sigma{h}) \times \prod_i{ -\frac{a_ib_ic_i}{(a_i+h/p_\alpha)(b_i+h/p_\alpha)(c_i+h/p_\alpha)}}, $$ - -$$ m_A=-36, n_A=0, o_A=3, p_A=2, $$ - -$$ m_R=2025, n_R=6, o_R=45/56, p_R=60^{1/3}, $$ - -$$ \chi = 2 \hat{\mathbf{r}}^T \mathbf{B}^{-1} -\hat{\mathbf{r}}, $$ - -$$ \hat{\mathbf{r}} = { \mathbf{r} } / |\mathbf{r}|, $$ - -$$ \mathbf{B} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 + -\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 $$ - -$$ \eta = \frac{ \det[\mathbf{S}_1]/\sigma_1^2+ -det[\mathbf{S}_2]/\sigma_2^2}{[\det[\mathbf{H}]/ -(\sigma_1+\sigma_2)]^{1/2}}, $$ - -$$ \sigma_i = (\hat{\mathbf{r}}^T\mathbf{A}_i^T\mathbf{S}_i^{-2} -\mathbf{A}_i\hat{\mathbf{r}})^{-1/2}, $$ - -$$ \mathbf{H} = \frac{1}{\sigma_1}\mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 + -\frac{1}{\sigma_2}\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$ - - -Here, we use the distance of closest approach approximation given by the -Perram reference, namely - -$$ h = |r| - \sigma_{12}, $$ - -$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}^T -\mathbf{G}^{-1} \hat{\mathbf{r}}]^{ -1/2 }, $$ - -and - -$$ \mathbf{G} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 + -\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$ - -\vspace{0.3in} - -The RE-squared anisotropic interaction between a -ellipsoidal particle and a Lennard-Jones sphere is defined -as the $\lim_{a_2->0}U$ under the constraints that -$a_2=b_2=c_2$ and $\frac{4}{3}\pi a_2^3\rho=1$: - -$$ U_{\mathrm{elj}}=U_{A_{\mathrm{elj}}}+U_{R_{\mathrm{elj}}}, $$ - -$$ U_{\alpha_{\mathrm{elj}}}=(\frac{3\sigma^3c_\alpha^3} -{4\pi h_{\mathrm{elj}}^3})\frac{A_{12_{\mathrm{elj}}}} -{m_\alpha}(\frac\sigma{h_{\mathrm{elj}}})^{n_\alpha} -(1+o_\alpha\chi_{\mathrm{elj}}\frac\sigma{h_{\mathrm{elj}}}) \times -\frac{a_1b_1c_1}{(a_1+h_{\mathrm{elj}}/p_\alpha) -(b_1+h_{\mathrm{elj}}/p_\alpha)(c_1+h_{\mathrm{elj}}/p_\alpha)}, $$ - -$$ A_{12_{\mathrm{elj}}}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3), $$ - -with $h_{\mathrm{elj}}$ and $\chi_{\mathrm{elj}}$ calculated as above -by replacing $B$ with $B_{\mathrm{elj}}$ and $G$ with $G_{\mathrm{elj}}$: - -$$ \mathbf{B}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 + I, $$ - -$$ \mathbf{G}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1.$$ - -\vspace{0.3in} - -The interaction between two LJ spheres is calculated as: - -$$ - U_{\mathrm{lj}} = 4 \epsilon \left[ \left(\frac{\sigma}{|\mathbf{r}|}\right)^{12} - - \left(\frac{\sigma}{|\mathbf{r}|}\right)^6 \right] -$$ - -\vspace{0.3in} - -The analytic derivatives are used for all force and torque calculation. - -\end{document} diff --git a/doc/doc2/Scripts/correlate.py b/doc/doc2/Scripts/correlate.py deleted file mode 100644 index 5a0aaaf2cc..0000000000 --- a/doc/doc2/Scripts/correlate.py +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env python -""" - function: - parse the block of thermo data in a lammps logfile and perform auto- and - cross correlation of the specified column data. The total sum of the - correlation is also computed which can be converted to an integral by - multiplying by the timestep. - output: - standard output contains column data for the auto- & cross correlations - plus the total sum of each. Note, only the upper triangle of the - correlation matrix is computed. - usage: - correlate.py [-c col] <-c col2> <-s max_correlation_time> [logfile] -""" -import sys -import re -import array - -# parse command line - -maxCorrelationTime = 0 -cols = array.array("I") -nCols = 0 -args = sys.argv[1:] -index = 0 -while index < len(args): - arg = args[index] - index += 1 - if (arg == "-c"): - cols.append(int(args[index])-1) - nCols += 1 - index += 1 - elif (arg == "-s"): - maxCorrelationTime = int(args[index]) - index += 1 - else : - filename = arg -if (nCols < 1): raise RuntimeError, 'no data columns requested' -data = [array.array("d")] -for s in range(1,nCols) : data.append( array.array("d") ) - -# read data block from log file - -start = False -input = open(filename) -nSamples = 0 -pattern = re.compile('\d') -line = input.readline() -while line : - columns = line.split() - if (columns and pattern.match(columns[0])) : - for i in range(nCols): - data[i].append( float(columns[cols[i]]) ) - nSamples += 1 - start = True - else : - if (start) : break - line = input.readline() -print "# read :",nSamples," samples of ", nCols," data" -if( maxCorrelationTime < 1): maxCorrelationTime = int(nSamples/2); - -# correlate and integrate - -correlationPairs = [] -for i in range(0,nCols): - for j in range(i,nCols): # note only upper triangle of the correlation matrix - correlationPairs.append([i,j]) -header = "# " -for k in range(len(correlationPairs)): - i = str(correlationPairs[k][0]+1) - j = str(correlationPairs[k][1]+1) - header += " C"+i+j+" sum_C"+i+j -print header -nCorrelationPairs = len(correlationPairs) -sum = [0.0] * nCorrelationPairs -for s in range(maxCorrelationTime) : - correlation = [0.0] * nCorrelationPairs - nt = nSamples-s - for t in range(0,nt) : - for p in range(nCorrelationPairs): - i = correlationPairs[p][0] - j = correlationPairs[p][1] - correlation[p] += data[i][t]*data[j][s+t] - output = "" - for p in range(0,nCorrelationPairs): - correlation[p] /= nt - sum[p] += correlation[p] - output += str(correlation[p]) + " " + str(sum[p]) + " " - print output diff --git a/doc/doc2/Section_accelerate.html b/doc/doc2/Section_accelerate.html deleted file mode 100644 index 28aaca1eaf..0000000000 --- a/doc/doc2/Section_accelerate.html +++ /dev/null @@ -1,420 +0,0 @@ - -

    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands - Next -Section -
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    5. Accelerating LAMMPS performance -

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    This section describes various methods for improving LAMMPS -performance for different classes of problems running on different -kinds of machines. -

    -

    There are two thrusts to the discussion that follows. The -first is using code options that implement alternate algorithms -that can speed-up a simulation. The second is to use one -of the several accelerator packages provided with LAMMPS that -contain code optimized for certain kinds of hardware, including -multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors. -

    - -

    The Benchmark page of the LAMMPS -web site gives performance results for the various accelerator -packages discussed in Section 5.2, for several of the standard LAMMPS -benchmark problems, as a function of problem size and number of -compute nodes, on different hardware platforms. -

    -
    - -
    - -

    5.1 Measuring performance -

    -

    Before trying to make your simulation run faster, you should -understand how it currently performs and where the bottlenecks are. -

    -

    The best way to do this is run the your system (actual number of -atoms) for a modest number of timesteps (say 100 steps) on several -different processor counts, including a single processor if possible. -Do this for an equilibrium version of your system, so that the -100-step timings are representative of a much longer run. There is -typically no need to run for 1000s of timesteps to get accurate -timings; you can simply extrapolate from short runs. -

    -

    For the set of runs, look at the timing data printed to the screen and -log file at the end of each LAMMPS run. This -section of the manual has an overview. -

    -

    Running on one (or a few processors) should give a good estimate of -the serial performance and what portions of the timestep are taking -the most time. Running the same problem on a few different processor -counts should give an estimate of parallel scalability. I.e. if the -simulation runs 16x faster on 16 processors, its 100% parallel -efficient; if it runs 8x faster on 16 processors, it's 50% efficient. -

    -

    The most important data to look at in the timing info is the timing -breakdown and relative percentages. For example, trying different -options for speeding up the long-range solvers will have little impact -if they only consume 10% of the run time. If the pairwise time is -dominating, you may want to look at GPU or OMP versions of the pair -style, as discussed below. Comparing how the percentages change as -you increase the processor count gives you a sense of how different -operations within the timestep are scaling. Note that if you are -running with a Kspace solver, there is additional output on the -breakdown of the Kspace time. For PPPM, this includes the fraction -spent on FFTs, which can be communication intensive. -

    -

    Another important detail in the timing info are the histograms of -atoms counts and neighbor counts. If these vary widely across -processors, you have a load-imbalance issue. This often results in -inaccurate relative timing data, because processors have to wait when -communication occurs for other processors to catch up. Thus the -reported times for "Communication" or "Other" may be higher than they -really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile -LAMMPS, to obtain synchronized timings. -

    -
    - -

    5.2 General strategies -

    -

    NOTE: this section 5.2 is still a work in progress -

    -

    Here is a list of general ideas for improving simulation performance. -Most of them are only applicable to certain models and certain -bottlenecks in the current performance, so let the timing data you -generate be your guide. It is hard, if not impossible, to predict how -much difference these options will make, since it is a function of -problem size, number of processors used, and your machine. There is -no substitute for identifying performance bottlenecks, and trying out -various options. -

    -
    • rRESPA -
    • 2-FFT PPPM -
    • Staggered PPPM -
    • single vs double PPPM -
    • partial charge PPPM -
    • verlet/split run style -
    • processor command for proc layout and numa layout -
    • load-balancing: balance and fix balance -
    -

    2-FFT PPPM, also called analytic differentiation or ad PPPM, uses -2 FFTs instead of the 4 FFTs used by the default ik differentiation -PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to -achieve the same accuracy as 4-FFT PPPM. For problems where the FFT -cost is the performance bottleneck (typically large problems running -on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. -

    -

    Staggered PPPM performs calculations using two different meshes, one -shifted slightly with respect to the other. This can reduce force -aliasing errors and increase the accuracy of the method, but also -doubles the amount of work required. For high relative accuracy, using -staggered PPPM allows one to half the mesh size in each dimension as -compared to regular PPPM, which can give around a 4x speedup in the -kspace time. However, for low relative accuracy, using staggered PPPM -gives little benefit and can be up to 2x slower in the kspace -time. For example, the rhodopsin benchmark was run on a single -processor, and results for kspace time vs. relative accuracy for the -different methods are shown in the figure below. For this system, -staggered PPPM (using ik differentiation) becomes useful when using a -relative accuracy of slightly greater than 1e-5 and above. -

    -
    -
    -

    IMPORTANT NOTE: Using staggered PPPM may not give the same increase in -accuracy of energy and pressure as it does in forces, so some caution -must be used if energy and/or pressure are quantities of interest, -such as when using a barostat. -

    -
    - -

    5.3 Packages with optimized styles -

    -

    Accelerated versions of various pair_style, -fixes, computes, and other commands have -been added to LAMMPS, which will typically run faster than the -standard non-accelerated versions. Some require appropriate hardware -to be present on your system, e.g. GPUs or Intel Xeon Phi -coprocessors. -

    -

    All of these commands are in packages provided with LAMMPS. An -overview of packages is give in Section -packages. -

    -

    These are the accelerator packages -currently in LAMMPS, either as standard or user packages: -

    -
    - - - - - -
    USER-CUDA for NVIDIA GPUs
    GPU for NVIDIA GPUs as well as OpenCL support
    USER-INTEL for Intel CPUs and Intel Xeon Phi
    KOKKOS for GPUs, Intel Xeon Phi, and OpenMP threading
    USER-OMP for OpenMP threading
    OPT generic CPU optimizations -
    - -

    Inverting this list, LAMMPS currently has acceleration support for -three kinds of hardware, via the listed packages: -

    -
    - - -
    Many-core CPUs USER-INTEL, KOKKOS, USER-OMP, OPT packages
    NVIDIA GPUs USER-CUDA, GPU, KOKKOS packages
    Intel Phi USER-INTEL, KOKKOS packages -
    - -

    Which package is fastest for your hardware may depend on the size -problem you are running and what commands (accelerated and -non-accelerated) are invoked by your input script. While these doc -pages include performance guidelines, there is no substitute for -trying out the different packages appropriate to your hardware. -

    -

    Any accelerated style has the same name as the corresponding standard -style, except that a suffix is appended. Otherwise, the syntax for -the command that uses the style is identical, their functionality is -the same, and the numerical results it produces should also be the -same, except for precision and round-off effects. -

    -

    For example, all of these styles are accelerated variants of the -Lennard-Jones pair_style lj/cut: -

    - -

    To see what accelerate styles are currently available, see -Section_commands 5 of the manual. The -doc pages for individual commands (e.g. pair lj/cut or -fix nve) also list any accelerated variants available -for that style. -

    -

    To use an accelerator package in LAMMPS, and one or more of the styles -it provides, follow these general steps. Details vary from package to -package and are explained in the individual accelerator doc pages, -listed above: -

    -
    - - - - - - - -
    build the accelerator library only for USER-CUDA and GPU packages
    install the accelerator package make yes-opt, make yes-user-intel, etc
    add compile/link flags to Makefile.machine in src/MAKE,
    only for USER-INTEL, KOKKOS, USER-OMP, OPT packages
    re-build LAMMPS make machine
    run a LAMMPS simulation lmp_machine < in.script
    mpirun -np 32 lmp_machine -in in.script
    enable the accelerator package via "-c on" and "-k on" command-line switches,
    only for USER-CUDA and KOKKOS packages
    set any needed options for the package via "-pk" command-line switch or package command,
    only if defaults need to be changed
    use accelerated styles in your input script via "-sf" command-line switch or suffix command -
    - -

    Note that the first 4 steps can be done as a single command, using the -src/Make.py tool. This tool is discussed in Section -2.4 of the manual, and its use is -illustrated in the individual accelerator sections. Typically these -steps only need to be done once, to create an executable that uses one -or more accelerator packages. -

    -

    The last 4 steps can all be done from the command-line when LAMMPS is -launched, without changing your input script, as illustrated in the -individual accelerator sections. Or you can add -package and suffix commands to your input -script. -

    -

    IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS -executable with all its accelerator packages installed. Note however -that the USER-INTEL and KOKKOS packages require you to choose one of -their hardware options when building for a specific platform. -I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP, -Cuda, or Phi option for the KOKKOS package. -

    -

    These are the exceptions. You cannot build a single executable with: -

    -
    • both the USER-INTEL Phi and KOKKOS Phi options -
    • the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages -
    -

    See the examples/accelerate/README and make.list files for sample -Make.py commands that build LAMMPS with any or all of the accelerator -packages. As an example, here is a command that builds with all the -GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda), -including settings to build the needed auxiliary USER-CUDA and GPU -libraries for Kepler GPUs: -

    -
    Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi   -cuda mode=double arch=35 -gpu mode=double arch=35 \  -kokkos cuda arch=35 lib-all file mpi 
-
    -

    The examples/accelerate directory also has input scripts that can be -used with all of the accelerator packages. See its README file for -details. -

    -

    Likewise, the bench directory has FERMI and KEPLER and PHI -sub-directories with Make.py commands and input scripts for using all -the accelerator packages on various machines. See the README files in -those dirs. -

    -

    As mentioned above, the Benchmark -page of the LAMMPS web site gives -performance results for the various accelerator packages for several -of the standard LAMMPS benchmark problems, as a function of problem -size and number of compute nodes, on different hardware platforms. -

    -

    Here is a brief summary of what the various packages provide. Details -are in the individual accelerator sections. -

    -
    • Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU -packages, and can be run on NVIDIA GPUs. The speed-up on a GPU -depends on a variety of factors, discussed in the accelerator -sections. - -
    • Styles with an "intel" suffix are part of the USER-INTEL -package. These styles support vectorized single and mixed precision -calculations, in addition to full double precision. In extreme cases, -this can provide speedups over 3.5x on CPUs. The package also -supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) -coprocessors. This can result in additional speedup over 2x depending -on the hardware configuration. - -
    • Styles with a "kk" suffix are part of the KOKKOS package, and can be -run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel -Xeon Phi in "native" mode. The speed-up depends on a variety of -factors, as discussed on the KOKKOS accelerator page. - -
    • Styles with an "omp" suffix are part of the USER-OMP package and allow -a pair-style to be run in multi-threaded mode using OpenMP. This can -be useful on nodes with high-core counts when using less MPI processes -than cores is advantageous, e.g. when running with PPPM so that FFTs -are run on fewer MPI processors or when the many MPI tasks would -overload the available bandwidth for communication. - -
    • Styles with an "opt" suffix are part of the OPT package and typically -speed-up the pairwise calculations of your simulation by 5-25% on a -CPU. -
    -

    The individual accelerator package doc pages explain: -

    -
    • what hardware and software the accelerated package requires -
    • how to build LAMMPS with the accelerated package -
    • how to run with the accelerated package either via command-line switches or modifying the input script -
    • speed-ups to expect -
    • guidelines for best performance -
    • restrictions -
    -
    - -

    5.4 Comparison of various accelerator packages -

    -

    NOTE: this section still needs to be re-worked with additional KOKKOS -and USER-INTEL information. -

    -

    The next section compares and contrasts the various accelerator -options, since there are multiple ways to perform OpenMP threading, -run on GPUs, and run on Intel Xeon Phi coprocessors. -

    -

    All 3 of these packages accelerate a LAMMPS calculation using NVIDIA -hardware, but they do it in different ways. -

    -

    As a consequence, for a particular simulation on specific hardware, -one package may be faster than the other. We give guidelines below, -but the best way to determine which package is faster for your input -script is to try both of them on your machine. See the benchmarking -section below for examples where this has been done. -

    -

    Guidelines for using each package optimally: -

    -
    • The GPU package allows you to assign multiple CPUs (cores) to a single -GPU (a common configuration for "hybrid" nodes that contain multicore -CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA -package does not allow this; you can only use one CPU per GPU. - -
    • The GPU package moves per-atom data (coordinates, forces) -back-and-forth between the CPU and GPU every timestep. The USER-CUDA -package only does this on timesteps when a CPU calculation is required -(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you -can formulate your input script to only use GPU-ized fixes and -computes, and avoid doing I/O too often (thermo output, dump file -snapshots, restart files), then the data transfer cost of the -USER-CUDA package can be very low, causing it to run faster than the -GPU package. - -
    • The GPU package is often faster than the USER-CUDA package, if the -number of atoms per GPU is smaller. The crossover point, in terms of -atoms/GPU at which the USER-CUDA package becomes faster depends -strongly on the pair style. For example, for a simple Lennard Jones -system the crossover (in single precision) is often about 50K-100K -atoms per GPU. When performing double precision calculations the -crossover point can be significantly smaller. - -
    • Both packages compute bonded interactions (bonds, angles, etc) on the -CPU. This means a model with bonds will force the USER-CUDA package -to transfer per-atom data back-and-forth between the CPU and GPU every -timestep. If the GPU package is running with several MPI processes -assigned to one GPU, the cost of computing the bonded interactions is -spread across more CPUs and hence the GPU package can run faster. - -
    • When using the GPU package with multiple CPUs assigned to one GPU, its -performance depends to some extent on high bandwidth between the CPUs -and the GPU. Hence its performance is affected if full 16 PCIe lanes -are not available for each GPU. In HPC environments this can be the -case if S2050/70 servers are used, where two devices generally share -one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide -full 16 lanes to each of the PCIe 2.0 16x slots. -
    -

    Differences between the two packages: -

    -
    • The GPU package accelerates only pair force, neighbor list, and PPPM -calculations. The USER-CUDA package currently supports a wider range -of pair styles and can also accelerate many fix styles and some -compute styles, as well as neighbor list and PPPM calculations. - -
    • The USER-CUDA package does not support acceleration for minimization. - -
    • The USER-CUDA package does not support hybrid pair styles. - -
    • The USER-CUDA package can order atoms in the neighbor list differently -from run to run resulting in a different order for force accumulation. - -
    • The USER-CUDA package has a limit on the number of atom types that can be -used in a simulation. - -
    • The GPU package requires neighbor lists to be built on the CPU when using -exclusion lists or a triclinic simulation box. - -
    • The GPU package uses more GPU memory than the USER-CUDA package. This -is generally not a problem since typical runs are computation-limited -rather than memory-limited. -
    -

    Examples: -

    -

    The LAMMPS distribution has two directories with sample input scripts -for the GPU and USER-CUDA packages. -

    -
    • lammps/examples/gpu = GPU package files -
    • lammps/examples/USER/cuda = USER-CUDA package files -
    -

    These contain input scripts for identical systems, so they can be used -to benchmark the performance of both packages on your system. -

    - diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html deleted file mode 100644 index 59d9427c5c..0000000000 --- a/doc/doc2/Section_commands.html +++ /dev/null @@ -1,669 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
    - - - - - - -
    - -

    3. Commands -

    -

    This section describes how a LAMMPS input script is formatted and the -input script commands used to define a LAMMPS simulation. -

    -3.1 LAMMPS input script
    -3.2 Parsing rules
    -3.3 Input script structure
    -3.4 Commands listed by category
    -3.5 Commands listed alphabetically
    - -
    - -
    - -

    3.1 LAMMPS input script -

    -

    LAMMPS executes by reading commands from a input script (text file), -one line at a time. When the input script ends, LAMMPS exits. Each -command causes LAMMPS to take some action. It may set an internal -variable, read in a file, or run a simulation. Most commands have -default settings, which means you only need to use the command if you -wish to change the default. -

    -

    In many cases, the ordering of commands in an input script is not -important. However the following rules apply: -

    -

    (1) LAMMPS does not read your entire input script and then perform a -simulation with all the settings. Rather, the input script is read -one line at a time and each command takes effect when it is read. -Thus this sequence of commands: -

    -
    timestep 0.5 
-run      100 
-run      100 
-
    -

    does something different than this sequence: -

    -
    run      100 
-timestep 0.5 
-run      100 
-
    -

    In the first case, the specified timestep (0.5 fmsec) is used for two -simulations of 100 timesteps each. In the 2nd case, the default -timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5 -fmsec timestep is used for the 2nd one. -

    -

    (2) Some commands are only valid when they follow other commands. For -example you cannot set the temperature of a group of atoms until atoms -have been defined and a group command is used to define which atoms -belong to the group. -

    -

    (3) Sometimes command B will use values that can be set by command A. -This means command A must precede command B in the input script if it -is to have the desired effect. For example, the -read_data command initializes the system by setting -up the simulation box and assigning atoms to processors. If default -values are not desired, the processors and -boundary commands need to be used before read_data to -tell LAMMPS how to map processors to the simulation box. -

    -

    Many input script errors are detected by LAMMPS and an ERROR or -WARNING message is printed. This section gives -more information on what errors mean. The documentation for each -command lists restrictions on how the command can be used. -

    -
    - -

    3.2 Parsing rules -

    -

    Each non-blank line in the input script is treated as a command. -LAMMPS commands are case sensitive. Command names are lower-case, as -are specified command arguments. Upper case letters may be used in -file names or user-chosen ID strings. -

    -

    Here is how each line in the input script is parsed by LAMMPS: -

    -

    (1) If the last printable character on the line is a "&" character, -the command is assumed to continue on the next line. The next line is -concatenated to the previous line by removing the "&" character and -line break. This allows long commands to be continued across two or -more lines. See the discussion of triple quotes in (6) for how to -continue a command across multiple line without using "&" characters. -

    -

    (2) All characters from the first "#" character onward are treated as -comment and discarded. See an exception in (6). Note that a -comment after a trailing "&" character will prevent the command from -continuing on the next line. Also note that for multi-line commands a -single leading "#" will comment out the entire command. -

    -

    (3) The line is searched repeatedly for $ characters, which indicate -variables that are replaced with a text string. See an exception in -(6). -

    -

    If the $ is followed by curly brackets, then the variable name is the -text inside the curly brackets. If no curly brackets follow the $, -then the variable name is the single character immediately following -the $. Thus ${myTemp} and $x refer to variable names "myTemp" and -"x". -

    -

    How the variable is converted to a text string depends on what style -of variable it is; see the variable doc page for details. -It can be a variable that stores multiple text strings, and return one -of them. The returned text string can be multiple "words" (space -separated) which will then be interpreted as multiple arguments in the -input command. The variable can also store a numeric formula which -will be evaluated and its numeric result returned as a string. -

    -

    As a special case, if the $ is followed by parenthesis, then the text -inside the parenthesis is treated as an "immediate" variable and -evaluated as an equal-style variable. This is a way -to use numeric formulas in an input script without having to assign -them to variable names. For example, these 3 input script lines: -

    -
    variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete 
-
    -

    can be replaced by -

    -
    region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE 
-
    -

    so that you do not have to define (or discard) a temporary variable X. -

    -

    Note that neither the curly-bracket or immediate form of variables can -contain nested $ characters for other variables to substitute for. -Thus you cannot do this: -

    -
    variable        a equal 2
-variable        b2 equal 4
-print           "B2 = ${b$a}" 
-
    -

    Nor can you specify this $($x-1.0) for an immediate variable, but -you could use $(v_x-1.0), since the latter is valid syntax for an -equal-style variable. -

    -

    See the variable command for more details of how -strings are assigned to variables and evaluated, and how they can be -used in input script commands. -

    -

    (4) The line is broken into "words" separated by whitespace (tabs, -spaces). Note that words can thus contain letters, digits, -underscores, or punctuation characters. -

    -

    (5) The first word is the command name. All successive words in the -line are arguments. -

    -

    (6) If you want text with spaces to be treated as a single argument, -it can be enclosed in either single or double or triple quotes. A -long single argument enclosed in single or double quotes can span -multiple lines if the "&" character is used, as described above. When -the lines are concatenated together (and the "&" characters and line -breaks removed), the text will become a single line. If you want -multiple lines of an argument to retain their line breaks, the text -can be enclosed in triple quotes, in which case "&" characters are not -needed. For example: -

    -
    print "Volume = $v"
-print 'Volume = $v'
-if "${steps} > 1000" then quit
-variable a string "red green blue &
-                   purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" 
-
    -

    In each case, the single, double, or triple quotes are removed when -the single argument they enclose is stored internally. -

    -

    See the dump modify format, print, -if, and python commands for examples. -

    -

    A "#" or "$" character that is between quotes will not be treated as a -comment indicator in (2) or substituted for as a variable in (3). -

    -

    IMPORTANT NOTE: If the argument is itself a command that requires a -quoted argument (e.g. using a print command as part of an -if or run every command), then single, double, or -triple quotes can be nested in the usual manner. See the doc pages -for those commands for examples. Only one of level of nesting is -allowed, but that should be sufficient for most use cases. -

    -
    - -

    3.3 Input script structure -

    -

    This section describes the structure of a typical LAMMPS input script. -The "examples" directory in the LAMMPS distribution contains many -sample input scripts; the corresponding problems are discussed in -Section_example, and animated on the LAMMPS -WWW Site. -

    -

    A LAMMPS input script typically has 4 parts: -

    -
    1. Initialization -
    2. Atom definition -
    3. Settings -
    4. Run a simulation -
    -

    The last 2 parts can be repeated as many times as desired. I.e. run a -simulation, change some settings, run some more, etc. Each of the 4 -parts is now described in more detail. Remember that almost all the -commands need only be used if a non-default value is desired. -

    -

    (1) Initialization -

    -

    Set parameters that need to be defined before atoms are created or -read-in from a file. -

    -

    The relevant commands are units, -dimension, newton, -processors, boundary, -atom_style, atom_modify. -

    -

    If force-field parameters appear in the files that will be read, these -commands tell LAMMPS what kinds of force fields are being used: -pair_style, bond_style, -angle_style, dihedral_style, -improper_style. -

    -

    (2) Atom definition -

    -

    There are 3 ways to define atoms in LAMMPS. Read them in from a data -or restart file via the read_data or -read_restart commands. These files can contain -molecular topology information. Or create atoms on a lattice (with no -molecular topology), using these commands: lattice, -region, create_box, -create_atoms. The entire set of atoms can be -duplicated to make a larger simulation using the -replicate command. -

    -

    (3) Settings -

    -

    Once atoms and molecular topology are defined, a variety of settings -can be specified: force field coefficients, simulation parameters, -output options, etc. -

    -

    Force field coefficients are set by these commands (they can also be -set in the read-in files): pair_coeff, -bond_coeff, angle_coeff, -dihedral_coeff, -improper_coeff, -kspace_style, dielectric, -special_bonds. -

    -

    Various simulation parameters are set by these commands: -neighbor, neigh_modify, -group, timestep, -reset_timestep, run_style, -min_style, min_modify. -

    -

    Fixes impose a variety of boundary conditions, time integration, and -diagnostic options. The fix command comes in many flavors. -

    -

    Various computations can be specified for execution during a -simulation using the compute, -compute_modify, and variable -commands. -

    -

    Output options are set by the thermo, dump, -and restart commands. -

    -

    (4) Run a simulation -

    -

    A molecular dynamics simulation is run using the run -command. Energy minimization (molecular statics) is performed using -the minimize command. A parallel tempering -(replica-exchange) simulation can be run using the -temper command. -

    -
    - -

    3.4 Commands listed by category -

    -

    This section lists all LAMMPS commands, grouped by category. The -next section lists the same commands alphabetically. Note -that some style options for some commands are part of specific LAMMPS -packages, which means they cannot be used unless the package was -included when LAMMPS was built. Not all packages are included in a -default LAMMPS build. These dependencies are listed as Restrictions -in the command's documentation. -

    -

    Initialization: -

    -

    atom_modify, atom_style, -boundary, dimension, -newton, processors, units -

    -

    Atom definition: -

    -

    create_atoms, create_box, -lattice, read_data, -read_dump, read_restart, -region, replicate -

    -

    Force fields: -

    -

    angle_coeff, angle_style, -bond_coeff, bond_style, -dielectric, dihedral_coeff, -dihedral_style, -improper_coeff, -improper_style, -kspace_modify, kspace_style, -pair_coeff, pair_modify, -pair_style, pair_write, -special_bonds -

    -

    Settings: -

    -

    comm_style, group, mass, -min_modify, min_style, -neigh_modify, neighbor, -reset_timestep, run_style, -set, timestep, velocity -

    -

    Fixes: -

    -

    fix, fix_modify, unfix -

    -

    Computes: -

    -

    compute, compute_modify, -uncompute -

    -

    Output: -

    -

    dump, dump image, -dump_modify, dump movie, -restart, thermo, -thermo_modify, thermo_style, -undump, write_data, -write_dump, write_restart -

    -

    Actions: -

    -

    delete_atoms, delete_bonds, -displace_atoms, change_box, -minimize, neb prd, -rerun, run, temper -

    -

    Miscellaneous: -

    -

    clear, echo, if, -include, jump, label, -log, next, print, -shell, variable -

    -
    - -

    3.5 Individual commands -

    -

    This section lists all LAMMPS commands alphabetically, with a separate -listing below of styles within certain commands. The previous -section lists the same commands, grouped by category. Note -that some style options for some commands are part of specific LAMMPS -packages, which means they cannot be used unless the package was -included when LAMMPS was built. Not all packages are included in a -default LAMMPS build. These dependencies are listed as Restrictions -in the command's documentation. -

    -
    - - - - - - - - - - - - - - - -
    angle_coeffangle_styleatom_modifyatom_stylebalancebond_coeff
    bond_styleboundaryboxchange_boxclearcomm_modify
    comm_stylecomputecompute_modifycreate_atomscreate_bondscreate_box
    delete_atomsdelete_bondsdielectricdihedral_coeffdihedral_styledimension
    displace_atomsdumpdump imagedump_modifydump movieecho
    fixfix_modifygroupifinfoimproper_coeff
    improper_styleincludejumpkspace_modifykspace_stylelabel
    latticelogmassminimizemin_modifymin_style
    moleculenebneigh_modifyneighbornewtonnext
    packagepair_coeffpair_modifypair_stylepair_writepartition
    prdprintprocessorspythonquitread_data
    read_dumpread_restartregionreplicatererunreset_timestep
    restartrunrun_stylesetshellspecial_bonds
    suffixtadtemperthermothermo_modifythermo_style
    timertimestepuncomputeundumpunfixunits
    variablevelocitywrite_datawrite_dumpwrite_restart -
    - -

    These are additional commands in USER packages, which can be used if -LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Fix styles -

    -

    See the fix command for one-line descriptions of each style -or click on the style itself for a full description. Some of the -styles have accelerated versions, which can be used if LAMMPS is built -with the appropriate accelerated package. -This is indicated by additional letters in parenthesis: c = USER-CUDA, -g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. -

    -
    - - - - - - - - - - - - - - -
    adaptaddforce (c)append/atomsatom/swapaveforce (c)ave/atomave/chunkave/correlate
    ave/histoave/histo/weightave/spatialave/timebalancebond/breakbond/createbond/swap
    box/relaxdeform (k)depositdragdt/resetefieldenforce2d (c)evaporate
    externalfreeze (c)gcmcgldgravity (co)heatindentlangevin (k)
    lineforcemomentummovemsstnebnph (ko)nphug (o)nph/asphere (o)
    nph/sphere (o)npt (cko)npt/asphere (o)npt/sphere (o)nve (cko)nve/aspherenve/asphere/noforcenve/body
    nve/limitnve/linenve/noforcenve/sphere (o)nve/trinvt (cko)nvt/asphere (o)nvt/sllod (o)
    nvt/sphere (o)onewayorient/fccplaneforcepoemspourpress/berendsenprint
    property/atomqeq/comb (o)qeq/dynamicqeq/pointqeq/shieldedqeq/slaterreax/bondsrecenter
    restrainrigid (o)rigid/nph (o)rigid/npt (o)rigid/nve (o)rigid/nvt (o)rigid/small (o)rigid/small/nph
    rigid/small/nptrigid/small/nverigid/small/nvtsetforce (c)shake (c)springspring/rgspring/self
    srdstore/forcestore/statetemp/berendsen (c)temp/csldtemp/csvrtemp/rescale (c)tfmc
    thermal/conductivitytmdttmtune/kspacevectorviscosityviscous (c)wall/colloid
    wall/granwall/harmonicwall/lj1043wall/lj126wall/lj93wall/pistonwall/reflect (k)wall/region
    wall/srd -
    - -

    These are additional fix styles in USER packages, which can be used if -LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Compute styles -

    -

    See the compute command for one-line descriptions of -each style or click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the appropriate accelerated -package. This is indicated by additional -letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. -

    - - -

    These are additional compute styles in USER packages, which can be -used if LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Pair_style potentials -

    -

    See the pair_style command for an overview of pair -potentials. Click on the style itself for a full description. Many -of the styles have accelerated versions, which can be used if LAMMPS -is built with the appropriate accelerated -package. This is indicated by additional -letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. -

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    nonehybridhybrid/overlayadp (o)
    airebo (o)beck (go)bodybop
    born (go)born/coul/long (cgo)born/coul/long/csborn/coul/msm (o)
    born/coul/wolf (go)brownian (o)brownian/poly (o)buck (cgko)
    buck/coul/cut (cgko)buck/coul/long (cgko)buck/coul/long/csbuck/coul/msm (o)
    buck/long/coul/long (o)colloid (go)comb (o)comb3
    coul/cut (gko)coul/debye (gko)coul/dsf (gko)coul/long (gko)
    coul/long/cscoul/msmcoul/streitzcoul/wolf (ko)
    dpd (o)dpd/tstat (o)dsmceam (cgkot)
    eam/alloy (cgkot)eam/fs (cgkot)eim (o)gauss (go)
    gayberne (gio)gran/hertz/history (o)gran/hooke (co)gran/hooke/history (o)
    hbond/dreiding/lj (o)hbond/dreiding/morse (o)kimlcbop
    line/lj (o)lj/charmm/coul/charmm (cko)lj/charmm/coul/charmm/implicit (cko)lj/charmm/coul/long (cgiko)
    lj/charmm/coul/msmlj/class2 (cgko)lj/class2/coul/cut (cko)lj/class2/coul/long (cgko)
    lj/cubic (go)lj/cut (cgikot)lj/cut/coul/cut (cgko)lj/cut/coul/debye (cgko)
    lj/cut/coul/dsf (gko)lj/cut/coul/long (cgikot)lj/cut/coul/long/cslj/cut/coul/msm (go)
    lj/cut/dipole/cut (go)lj/cut/dipole/longlj/cut/tip4p/cut (o)lj/cut/tip4p/long (ot)
    lj/expand (cgko)lj/gromacs (cgko)lj/gromacs/coul/gromacs (cko)lj/long/coul/long (o)
    lj/long/dipole/longlj/long/tip4p/longlj/smooth (co)lj/smooth/linear (o)
    lj96/cut (cgo)lubricate (o)lubricate/poly (o)lubricateU
    lubricateU/polymeam (o)mie/cut (o)morse (cgot)
    nb3b/harmonic (o)nm/cut (o)nm/cut/coul/cut (o)nm/cut/coul/long (o)
    peri/epsperi/lps (o)peri/pmb (o)peri/ves
    polymorphicreaxrebo (o)resquared (go)
    snapsoft (go)sw (cgkio)table (gko)
    tersoff (cgko)tersoff/mod (ko)tersoff/zbl (ko)tip4p/cut (o)
    tip4p/long (o)tri/lj (o)vashishta (o)yukawa (go)
    yukawa/colloid (go)zbl (go) -
    - -

    These are additional pair styles in USER packages, which can be used -if LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Bond_style potentials -

    -

    See the bond_style command for an overview of bond -potentials. Click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the appropriate accelerated -package. This is indicated by additional -letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. -

    - - -

    These are additional bond styles in USER packages, which can be used -if LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Angle_style potentials -

    -

    See the angle_style command for an overview of -angle potentials. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the appropriate accelerated -package. This is indicated by additional -letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. -

    - - -

    These are additional angle styles in USER packages, which can be used -if LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Dihedral_style potentials -

    -

    See the dihedral_style command for an overview -of dihedral potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the appropriate accelerated -package. This is indicated by additional -letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. -

    - - -

    These are additional dihedral styles in USER packages, which can be -used if LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Improper_style potentials -

    -

    See the improper_style command for an overview -of improper potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the appropriate accelerated -package. This is indicated by additional -letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. -

    - - -

    These are additional improper styles in USER packages, which can be -used if LAMMPS is built with the appropriate -package. -

    - - -
    - -

    Kspace solvers -

    -

    See the kspace_style command for an overview of -Kspace solvers. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the appropriate accelerated -package. This is indicated by additional -letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. -

    - - - diff --git a/doc/doc2/Section_errors.html b/doc/doc2/Section_errors.html deleted file mode 100644 index 699531acca..0000000000 --- a/doc/doc2/Section_errors.html +++ /dev/null @@ -1,11168 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands - Next -Section -
    - - - - - - -
    - -

    12. Errors -

    -

    This section describes the errors you can encounter when using LAMMPS, -either conceptually, or as printed out by the program. -

    -12.1 Common problems
    -12.2 Reporting bugs
    -12.3 Error & warning messages
    - -
    - -
    - -

    12.1 Common problems -

    -

    If two LAMMPS runs do not produce the same answer on different -machines or different numbers of processors, this is typically not a -bug. In theory you should get identical answers on any number of -processors and on any machine. In practice, numerical round-off can -cause slight differences and eventual divergence of molecular dynamics -phase space trajectories within a few 100s or few 1000s of timesteps. -However, the statistical properties of the two runs (e.g. average -energy or temperature) should still be the same. -

    -

    If the velocity command is used to set initial atom -velocities, a particular atom can be assigned a different velocity -when the problem is run on a different number of processors or on -different machines. If this happens, the phase space trajectories of -the two simulations will rapidly diverge. See the discussion of the -loop option in the velocity command for details and -options that avoid this issue. -

    -

    Similarly, the create_atoms command generates a -lattice of atoms. For the same physical system, the ordering and -numbering of atoms by atom ID may be different depending on the number -of processors. -

    -

    Some commands use random number generators which may be setup to -produce different random number streams on each processor and hence -will produce different effects when run on different numbers of -processors. A commonly-used example is the fix -langevin command for thermostatting. -

    -

    A LAMMPS simulation typically has two stages, setup and run. Most -LAMMPS errors are detected at setup time; others like a bond -stretching too far may not occur until the middle of a run. -

    -

    LAMMPS tries to flag errors and print informative error messages so -you can fix the problem. Of course, LAMMPS cannot figure out your -physics or numerical mistakes, like choosing too big a timestep, -specifying erroneous force field coefficients, or putting 2 atoms on -top of each other! If you run into errors that LAMMPS doesn't catch -that you think it should flag, please send an email to the -developers. -

    -

    If you get an error message about an invalid command in your input -script, you can determine what command is causing the problem by -looking in the log.lammps file or using the echo command -to see it on the screen. If you get an error like "Invalid ... -style", with ... being fix, compute, pair, etc, it means that you -mistyped the style name or that the command is part of an optional -package which was not compiled into your executable. The list of -available styles in your executable can be listed by using the -h -command-line argument. The installation -and compilation of optional packages is explained in the installation -instructions. -

    -

    For a given command, LAMMPS expects certain arguments in a specified -order. If you mess this up, LAMMPS will often flag the error, but it -may also simply read a bogus argument and assign a value that is -valid, but not what you wanted. E.g. trying to read the string "abc" -as an integer value of 0. Careful reading of the associated doc page -for the command should allow you to fix these problems. Note that -some commands allow for variables to be specified in place of numeric -constants so that the value can be evaluated and change over the -course of a run. This is typically done with the syntax v_name for -a parameter, where name is the name of the variable. This is only -allowed if the command documentation says it is. -

    -

    Generally, LAMMPS will print a message to the screen and logfile and -exit gracefully when it encounters a fatal error. Sometimes it will -print a WARNING to the screen and logfile and continue on; you can -decide if the WARNING is important or not. A WARNING message that is -generated in the middle of a run is only printed to the screen, not to -the logfile, to avoid cluttering up thermodynamic output. If LAMMPS -crashes or hangs without spitting out an error message first then it -could be a bug (see this section) or one of the following -cases: -

    -

    LAMMPS runs in the available memory a processor allows to be -allocated. Most reasonable MD runs are compute limited, not memory -limited, so this shouldn't be a bottleneck on most platforms. Almost -all large memory allocations in the code are done via C-style malloc's -which will generate an error message if you run out of memory. -Smaller chunks of memory are allocated via C++ "new" statements. If -you are unlucky you could run out of memory just when one of these -small requests is made, in which case the code will crash or hang (in -parallel), since LAMMPS doesn't trap on those errors. -

    -

    Illegal arithmetic can cause LAMMPS to run slow or crash. This is -typically due to invalid physics and numerics that your simulation is -computing. If you see wild thermodynamic values or NaN values in your -LAMMPS output, something is wrong with your simulation. If you -suspect this is happening, it is a good idea to print out -thermodynamic info frequently (e.g. every timestep) via the -thermo so you can monitor what is happening. -Visualizing the atom movement is also a good idea to insure your model -is behaving as you expect. -

    -

    In parallel, one way LAMMPS can hang is due to how different MPI -implementations handle buffering of messages. If the code hangs -without an error message, it may be that you need to specify an MPI -setting or two (usually via an environment variable) to enable -buffering or boost the sizes of messages that can be buffered. -

    -
    - -

    12.2 Reporting bugs -

    -

    If you are confident that you have found a bug in LAMMPS, follow these -steps. -

    -

    Check the New features and bug -fixes section of the LAMMPS WWW -site to see if the bug has already been reported or fixed or the -Unfixed bug to see if a fix is -pending. -

    -

    Check the mailing list -to see if it has been discussed before. -

    -

    If not, send an email to the mailing list describing the problem with -any ideas you have as to what is causing it or where in the code the -problem might be. The developers will ask for more info if needed, -such as an input script or data files. -

    -

    The most useful thing you can do to help us fix the bug is to isolate -the problem. Run it on the smallest number of atoms and fewest number -of processors and with the simplest input script that reproduces the -bug and try to identify what command or combination of commands is -causing the problem. -

    -

    As a last resort, you can send an email directly to the -developers. -

    -
    - -

    12.3 Error & warning messages -

    -

    These are two alphabetic lists of the ERROR and -WARNING messages LAMMPS prints out and the reason why. If the -explanation here is not sufficient, the documentation for the -offending command may help. -Error and warning messages also list the source file and line number -where the error was generated. For example, this message -

    -

    ERROR: Illegal velocity command (velocity.cpp:78) -

    -

    means that line #78 in the file src/velocity.cpp generated the error. -Looking in the source code may help you figure out what went wrong. -

    -

    Note that error messages from user-contributed -packages are not listed here. If such an -error occurs and is not self-explanatory, you'll need to look in the -source code or contact the author of the package. -

    -

    Errors: -

    -
    - -
    1-3 bond count is inconsistent - -
    An inconsistency was detected when computing the number of 1-3 -neighbors for each atom. This likely means something is wrong with -the bond topologies you have defined. - -
    1-4 bond count is inconsistent - -
    An inconsistency was detected when computing the number of 1-4 -neighbors for each atom. This likely means something is wrong with -the bond topologies you have defined. - -
    Accelerator sharing is not currently supported on system - -
    Multiple MPI processes cannot share the accelerator on your -system. For NVIDIA GPUs, see the nvidia-smi command to change this -setting. - -
    All angle coeffs are not set - -
    All angle coefficients must be set in the data file or by the -angle_coeff command before running a simulation. - -
    All atoms of a swapped type must have the same charge. - -
    Self-explanatory. - -
    All bond coeffs are not set - -
    All bond coefficients must be set in the data file or by the -bond_coeff command before running a simulation. - -
    All dihedral coeffs are not set - -
    All dihedral coefficients must be set in the data file or by the -dihedral_coeff command before running a simulation. - -
    All improper coeffs are not set - -
    All improper coefficients must be set in the data file or by the -improper_coeff command before running a simulation. - -
    All masses are not set - -
    For atom styles that define masses for each atom type, all masses must -be set in the data file or by the mass command before running a -simulation. They must also be set before using the velocity -command. - -
    All mol IDs should be set for fix gcmc group atoms - -
    The molecule flag is on, yet not all molecule ids in the fix group -have been set to non-zero positive values by the user. This is an -error since all atoms in the fix gcmc group are eligible for deletion, -rotation, and translation and therefore must have valid molecule ids. - -
    All pair coeffs are not set - -
    All pair coefficients must be set in the data file or by the -pair_coeff command before running a simulation. - -
    All read_dump x,y,z fields must be specified for scaled, triclinic coords - -
    For triclinic boxes and scaled coordinates you must specify all 3 of -the x,y,z fields, else LAMMPS cannot reconstruct the unscaled -coordinates. - -
    All universe/uloop variables must have same # of values - -
    Self-explanatory. - -
    All variables in next command must be same style - -
    Self-explanatory. - -
    Angle atom missing in delete_bonds - -
    The delete_bonds command cannot find one or more atoms in a particular -angle on a particular processor. The pairwise cutoff is too short or -the atoms are too far apart to make a valid angle. - -
    Angle atom missing in set command - -
    The set command cannot find one or more atoms in a particular angle on -a particular processor. The pairwise cutoff is too short or the atoms -are too far apart to make a valid angle. - -
    Angle atoms %d %d %d missing on proc %d at step %ld - -
    One or more of 3 atoms needed to compute a particular angle are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the angle has blown apart and an atom is -too far away. - -
    Angle atoms missing on proc %d at step %ld - -
    One or more of 3 atoms needed to compute a particular angle are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the angle has blown apart and an atom is -too far away. - -
    Angle coeff for hybrid has invalid style - -
    Angle style hybrid uses another angle style as one of its -coefficients. The angle style used in the angle_coeff command or read -from a restart file is not recognized. - -
    Angle coeffs are not set - -
    No angle coefficients have been assigned in the data file or via the -angle_coeff command. - -
    Angle extent > half of periodic box length - -
    This error was detected by the neigh_modify check yes setting. It is -an error because the angle atoms are so far apart it is ambiguous how -it should be defined. - -
    Angle potential must be defined for SHAKE - -
    When shaking angles, an angle_style potential must be used. - -
    Angle style hybrid cannot have hybrid as an argument - -
    Self-explanatory. - -
    Angle style hybrid cannot have none as an argument - -
    Self-explanatory. - -
    Angle style hybrid cannot use same angle style twice - -
    Self-explanatory. - -
    Angle table must range from 0 to 180 degrees - -
    Self-explanatory. - -
    Angle table parameters did not set N - -
    List of angle table parameters must include N setting. - -
    Angle_coeff command before angle_style is defined - -
    Coefficients cannot be set in the data file or via the angle_coeff -command until an angle_style has been assigned. - -
    Angle_coeff command before simulation box is defined - -
    The angle_coeff command cannot be used before a read_data, -read_restart, or create_box command. - -
    Angle_coeff command when no angles allowed - -
    The chosen atom style does not allow for angles to be defined. - -
    Angle_style command when no angles allowed - -
    The chosen atom style does not allow for angles to be defined. - -
    Angles assigned incorrectly - -
    Angles read in from the data file were not assigned correctly to -atoms. This means there is something invalid about the topology -definitions. - -
    Angles defined but no angle types - -
    The data file header lists angles but no angle types. - -
    Append boundary must be shrink/minimum - -
    The boundary style of the face where atoms are added -must be of type m (shrink/minimum). - -
    Arccos of invalid value in variable formula - -
    Argument of arccos() must be between -1 and 1. - -
    Arcsin of invalid value in variable formula - -
    Argument of arcsin() must be between -1 and 1. - -
    Assigning body parameters to non-body atom - -
    Self-explanatory. - -
    Assigning ellipsoid parameters to non-ellipsoid atom - -
    Self-explanatory. - -
    Assigning line parameters to non-line atom - -
    Self-explanatory. - -
    Assigning tri parameters to non-tri atom - -
    Self-explanatory. - -
    Atom ID is negative - -
    Self-explanatory. - -
    Atom ID is too big - -
    The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL -setting in your Makefile. See Section_start 2.2 of the manual for -more details. - -
    Atom ID is zero - -
    Either all atoms IDs must be zero or none of them. - -
    Atom IDs must be consecutive for velocity create loop all - -
    Self-explanatory. - -
    Atom IDs must be used for molecular systems - -
    Atom IDs are used to identify and find partner atoms in bonds. - -
    Atom count changed in fix neb - -
    This is not allowed in a NEB calculation. - -
    Atom count is inconsistent, cannot write data file - -
    The sum of atoms across processors does not equal the global number -of atoms. Probably some atoms have been lost. - -
    Atom count is inconsistent, cannot write restart file - -
    Sum of atoms across processors does not equal initial total count. -This is probably because you have lost some atoms. - -
    Atom in too many rigid bodies - boost MAXBODY - -
    Fix poems has a parameter MAXBODY (in fix_poems.cpp) which determines -the maximum number of rigid bodies a single atom can belong to (i.e. a -multibody joint). The bodies you have defined exceed this limit. - -
    Atom sort did not operate correctly - -
    This is an internal LAMMPS error. Please report it to the -developers. - -
    Atom sorting has bin size = 0.0 - -
    The neighbor cutoff is being used as the bin size, but it is zero. -Thus you must explicitly list a bin size in the atom_modify sort -command or turn off sorting. - -
    Atom style hybrid cannot have hybrid as an argument - -
    Self-explanatory. - -
    Atom style hybrid cannot use same atom style twice - -
    Self-explanatory. - -
    Atom style template molecule must have atom types - -
    The defined molecule(s) does not specify atom types. - -
    Atom style was redefined after using fix property/atom - -
    This is not allowed. - -
    Atom vector in equal-style variable formula - -
    Atom vectors generate one value per atom which is not allowed -in an equal-style variable. - -
    Atom-style variable in equal-style variable formula - -
    Atom-style variables generate one value per atom which is not allowed -in an equal-style variable. - -
    Atom_modify id command after simulation box is defined - -
    The atom_modify id command cannot be used after a read_data, -read_restart, or create_box command. - -
    Atom_modify map command after simulation box is defined - -
    The atom_modify map command cannot be used after a read_data, -read_restart, or create_box command. - -
    Atom_modify sort and first options cannot be used together - -
    Self-explanatory. - -
    Atom_style command after simulation box is defined - -
    The atom_style command cannot be used after a read_data, -read_restart, or create_box command. - -
    Atom_style line can only be used in 2d simulations - -
    Self-explanatory. - -
    Atom_style tri can only be used in 3d simulations - -
    Self-explanatory. - -
    Atomfile variable could not read values - -
    Check the file assigned to the variable. - -
    Atomfile variable in equal-style variable formula - -
    Self-explanatory. - -
    Atomfile-style variable in equal-style variable formula - -
    Self-explanatory. - -
    Attempt to pop empty stack in fix box/relax - -
    Internal LAMMPS error. Please report it to the developers. - -
    Attempt to push beyond stack limit in fix box/relax - -
    Internal LAMMPS error. Please report it to the developers. - -
    Attempting to rescale a 0.0 temperature - -
    Cannot rescale a temperature that is already 0.0. - -
    Bad FENE bond - -
    Two atoms in a FENE bond have become so far apart that the bond cannot -be computed. - -
    Bad TIP4P angle type for PPPM/TIP4P - -
    Specified angle type is not valid. - -
    Bad TIP4P angle type for PPPMDisp/TIP4P - -
    Specified angle type is not valid. - -
    Bad TIP4P bond type for PPPM/TIP4P - -
    Specified bond type is not valid. - -
    Bad TIP4P bond type for PPPMDisp/TIP4P - -
    Specified bond type is not valid. - -
    Bad fix ID in fix append/atoms command - -
    The value of the fix_id for keyword spatial must start with the suffix -f_. - -
    Bad grid of processors - -
    The 3d grid of processors defined by the processors command does not -match the number of processors LAMMPS is being run on. - -
    Bad kspace_modify kmax/ewald parameter - -
    Kspace_modify values for the kmax/ewald keyword must be integers > 0 - -
    Bad kspace_modify slab parameter - -
    Kspace_modify value for the slab/volume keyword must be >= 2.0. - -
    Bad matrix inversion in mldivide3 - -
    This error should not occur unless the matrix is badly formed. - -
    Bad principal moments - -
    Fix rigid did not compute the principal moments of inertia of a rigid -group of atoms correctly. - -
    Bad quadratic solve for particle/line collision - -
    This is an internal error. It should nornally not occur. - -
    Bad quadratic solve for particle/tri collision - -
    This is an internal error. It should nornally not occur. - -
    Bad real space Coulomb cutoff in fix tune/kspace - -
    Fix tune/kspace tried to find the optimal real space Coulomb cutoff using -the Newton-Rhaphson method, but found a non-positive or NaN cutoff - -
    Balance command before simulation box is defined - -
    The balance command cannot be used before a read_data, read_restart, -or create_box command. - -
    Balance produced bad splits - -
    This should not occur. It means two or more cutting plane locations -are on top of each other or out of order. Report the problem to the -developers. - -
    Balance rcb cannot be used with comm_style brick - -
    Comm_style tiled must be used instead. - -
    Balance shift string is invalid - -
    The string can only contain the characters "x", "y", or "z". - -
    Bias compute does not calculate a velocity bias - -
    The specified compute must compute a bias for temperature. - -
    Bias compute does not calculate temperature - -
    The specified compute must compute temperature. - -
    Bias compute group does not match compute group - -
    The specified compute must operate on the same group as the parent -compute. - -
    Big particle in fix srd cannot be point particle - -
    Big particles must be extended spheriods or ellipsoids. - -
    Bigint setting in lmptype.h is invalid - -
    Size of bigint is less than size of tagint. - -
    Bigint setting in lmptype.h is not compatible - -
    Format of bigint stored in restart file is not consistent with LAMMPS -version you are running. See the settings in src/lmptype.h - -
    Bitmapped lookup tables require int/float be same size - -
    Cannot use pair tables on this machine, because of word sizes. Use -the pair_modify command with table 0 instead. - -
    Bitmapped table in file does not match requested table - -
    Setting for bitmapped table in pair_coeff command must match table -in file exactly. - -
    Bitmapped table is incorrect length in table file - -
    Number of table entries is not a correct power of 2. - -
    Bond and angle potentials must be defined for TIP4P - -
    Cannot use TIP4P pair potential unless bond and angle potentials -are defined. - -
    Bond atom missing in box size check - -
    The 2nd atoms needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. - -
    Bond atom missing in delete_bonds - -
    The delete_bonds command cannot find one or more atoms in a particular -bond on a particular processor. The pairwise cutoff is too short or -the atoms are too far apart to make a valid bond. - -
    Bond atom missing in image check - -
    The 2nd atom in a particular bond is missing on this processor. -Typically this is because the pairwise cutoff is set too short or the -bond has blown apart and an atom is too far away. - -
    Bond atom missing in set command - -
    The set command cannot find one or more atoms in a particular bond on -a particular processor. The pairwise cutoff is too short or the atoms -are too far apart to make a valid bond. - -
    Bond atoms %d %d missing on proc %d at step %ld - -
    The 2nd atom needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. - -
    Bond atoms missing on proc %d at step %ld - -
    The 2nd atom needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. - -
    Bond coeff for hybrid has invalid style - -
    Bond style hybrid uses another bond style as one of its coefficients. -The bond style used in the bond_coeff command or read from a restart -file is not recognized. - -
    Bond coeffs are not set - -
    No bond coefficients have been assigned in the data file or via the -bond_coeff command. - -
    Bond extent > half of periodic box length - -
    This error was detected by the neigh_modify check yes setting. It is -an error because the bond atoms are so far apart it is ambiguous how -it should be defined. - -
    Bond potential must be defined for SHAKE - -
    Cannot use fix shake unless bond potential is defined. - -
    Bond style hybrid cannot have hybrid as an argument - -
    Self-explanatory. - -
    Bond style hybrid cannot have none as an argument - -
    Self-explanatory. - -
    Bond style hybrid cannot use same bond style twice - -
    Self-explanatory. - -
    Bond style quartic cannot be used with 3,4-body interactions - -
    No angle, dihedral, or improper styles can be defined when using -bond style quartic. - -
    Bond style quartic cannot be used with atom style template - -
    This bond style can change the bond topology which is not -allowed with this atom style. - -
    Bond style quartic requires special_bonds = 1,1,1 - -
    This is a restriction of the current bond quartic implementation. - -
    Bond table parameters did not set N - -
    List of bond table parameters must include N setting. - -
    Bond table values are not increasing - -
    The values in the tabulated file must be monotonically increasing. - -
    BondAngle coeff for hybrid angle has invalid format - -
    No "ba" field should appear in data file entry. - -
    BondBond coeff for hybrid angle has invalid format - -
    No "bb" field should appear in data file entry. - -
    Bond_coeff command before bond_style is defined - -
    Coefficients cannot be set in the data file or via the bond_coeff -command until an bond_style has been assigned. - -
    Bond_coeff command before simulation box is defined - -
    The bond_coeff command cannot be used before a read_data, -read_restart, or create_box command. - -
    Bond_coeff command when no bonds allowed - -
    The chosen atom style does not allow for bonds to be defined. - -
    Bond_style command when no bonds allowed - -
    The chosen atom style does not allow for bonds to be defined. - -
    Bonds assigned incorrectly - -
    Bonds read in from the data file were not assigned correctly to atoms. -This means there is something invalid about the topology definitions. - -
    Bonds defined but no bond types - -
    The data file header lists bonds but no bond types. - -
    Both restart files must use % or neither - -
    Self-explanatory. - -
    Both restart files must use MPI-IO or neither - -
    Self-explanatory. - -
    Both sides of boundary must be periodic - -
    Cannot specify a boundary as periodic only on the lo or hi side. Must -be periodic on both sides. - -
    Boundary command after simulation box is defined - -
    The boundary command cannot be used after a read_data, read_restart, -or create_box command. - -
    Box bounds are invalid - -
    The box boundaries specified in the read_data file are invalid. The -lo value must be less than the hi value for all 3 dimensions. - -
    Box command after simulation box is defined - -
    The box command cannot be used after a read_data, read_restart, or -create_box command. - -
    CPU neighbor lists must be used for ellipsoid/sphere mix. - -
    When using Gay-Berne or RE-squared pair styles with both ellipsoidal and -spherical particles, the neighbor list must be built on the CPU - -
    Can not specify Pxy/Pxz/Pyz in fix box/relax with non-triclinic box - -
    Only triclinic boxes can be used with off-diagonal pressure components. -See the region prism command for details. - -
    Can not specify Pxy/Pxz/Pyz in fix nvt/npt/nph with non-triclinic box - -
    Only triclinic boxes can be used with off-diagonal pressure components. -See the region prism command for details. - -
    Can only use -plog with multiple partitions - -
    Self-explanatory. See doc page discussion of command-line switches. - -
    Can only use -pscreen with multiple partitions - -
    Self-explanatory. See doc page discussion of command-line switches. - -
    Can only use NEB with 1-processor replicas - -
    This is current restriction for NEB as implemented in LAMMPS. - -
    Can only use TAD with 1-processor replicas for NEB - -
    This is current restriction for NEB as implemented in LAMMPS. - -
    Cannot (yet) do analytic differentiation with pppm/gpu - -
    This is a current restriction of this command. - -
    Cannot (yet) use 'electron' units with dipoles - -
    This feature is not yet supported. - -
    Cannot (yet) use Ewald with triclinic box and slab correction - -
    This feature is not yet supported. - -
    Cannot (yet) use K-space slab correction with compute group/group for triclinic systems - -
    This option is not yet supported. - -
    Cannot (yet) use MSM with 2d simulation - -
    This feature is not yet supported. - -
    Cannot (yet) use PPPM with triclinic box and TIP4P - -
    This feature is not yet supported. - -
    Cannot (yet) use PPPM with triclinic box and kspace_modify diff ad - -
    This feature is not yet supported. - -
    Cannot (yet) use PPPM with triclinic box and slab correction - -
    This feature is not yet supported. - -
    Cannot (yet) use kspace slab correction with long-range dipoles and non-neutral systems or per-atom energy - -
    This feature is not yet supported. - -
    Cannot (yet) use kspace_modify diff ad with compute group/group - -
    This option is not yet supported. - -
    Cannot (yet) use kspace_style pppm/stagger with triclinic systems - -
    This feature is not yet supported. - -
    Cannot (yet) use molecular templates with Kokkos - -
    Self-explanatory. - -
    Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile) - -
    Single precision cannot be used with MSM. - -
    Cannot add atoms to fix move variable - -
    Atoms can not be added afterwards to this fix option. - -
    Cannot append atoms to a triclinic box - -
    The simulation box must be defined with edges alligned with the -Cartesian axes. - -
    Cannot balance in z dimension for 2d simulation - -
    Self-explanatory. - -
    Cannot change box ortho/triclinic with certain fixes defined - -
    This is because those fixes store the shape of the box. You need to -use unfix to discard the fix, change the box, then redefine a new -fix. - -
    Cannot change box ortho/triclinic with dumps defined - -
    This is because some dumps store the shape of the box. You need to -use undump to discard the dump, change the box, then redefine a new -dump. - -
    Cannot change box tilt factors for orthogonal box - -
    Cannot use tilt factors unless the simulation box is non-orthogonal. - -
    Cannot change box to orthogonal when tilt is non-zero - -
    Self-explanatory. - -
    Cannot change box z boundary to nonperiodic for a 2d simulation - -
    Self-explanatory. - -
    Cannot change dump_modify every for dump dcd - -
    The frequency of writing dump dcd snapshots cannot be changed. - -
    Cannot change dump_modify every for dump xtc - -
    The frequency of writing dump xtc snapshots cannot be changed. - -
    Cannot change timestep once fix srd is setup - -
    This is because various SRD properties depend on the timestep -size. - -
    Cannot change timestep with fix pour - -
    This is because fix pour pre-computes the time delay for particles to -fall out of the insertion volume due to gravity. - -
    Cannot change to comm_style brick from tiled layout - -
    Self-explanatory. - -
    Cannot change_box after reading restart file with per-atom info - -
    This is because the restart file info cannot be migrated with the -atoms. You can get around this by performing a 0-timestep run which -will assign the restart file info to actual atoms. - -
    Cannot change_box in xz or yz for 2d simulation - -
    Self-explanatory. - -
    Cannot change_box in z dimension for 2d simulation - -
    Self-explanatory. - -
    Cannot clear group all - -
    This operation is not allowed. - -
    Cannot close restart file - MPI error: %s - -
    This error was generated by MPI when reading/writing an MPI-IO restart -file. - -
    Cannot compute initial g_ewald_disp - -
    LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6 -factor that partitions the computation between real space and k-space -for Disptersion interactions. - -
    Cannot create an atom map unless atoms have IDs - -
    The simulation requires a mapping from global atom IDs to local atoms, -but the atoms that have been defined have no IDs. - -
    Cannot create atoms with undefined lattice - -
    Must use the lattice command before using the create_atoms -command. - -
    Cannot create/grow a vector/array of pointers for %s - -
    LAMMPS code is making an illegal call to the templated memory -allocaters, to create a vector or array of pointers. - -
    Cannot create_atoms after reading restart file with per-atom info - -
    The per-atom info was stored to be used when by a fix that you may -re-define. If you add atoms before re-defining the fix, then there -will not be a correct amount of per-atom info. - -
    Cannot create_box after simulation box is defined - -
    A simulation box can only be defined once. - -
    Cannot currently use pair reax with pair hybrid - -
    This is not yet supported. - -
    Cannot currently use pppm/gpu with fix balance. - -
    Self-explanatory. - -
    Cannot delete group all - -
    Self-explanatory. - -
    Cannot delete group currently used by a compute - -
    Self-explanatory. - -
    Cannot delete group currently used by a dump - -
    Self-explanatory. - -
    Cannot delete group currently used by a fix - -
    Self-explanatory. - -
    Cannot delete group currently used by atom_modify first - -
    Self-explanatory. - -
    Cannot delete_atoms bond yes for non-molecular systems - -
    Self-explanatory. - -
    Cannot delete_atoms mol yes for non-molecular systems - -
    Self-explanatory. - -
    Cannot displace_atoms after reading restart file with per-atom info - -
    This is because the restart file info cannot be migrated with the -atoms. You can get around this by performing a 0-timestep run which -will assign the restart file info to actual atoms. - -
    Cannot do GCMC on atoms in atom_modify first group - -
    This is a restriction due to the way atoms are organized in a list to -enable the atom_modify first command. - -
    Cannot do atom/swap on atoms in atom_modify first group - -
    This is a restriction due to the way atoms are organized in a list to -enable the atom_modify first command. - -
    Cannot dump sort on atom IDs with no atom IDs defined - -
    Self-explanatory. - -
    Cannot dump sort when multiple dump files are written - -
    In this mode, each processor dumps its atoms to a file, so -no sorting is allowed. - -
    Cannot embed Python when also extending Python with LAMMPS - -
    When running LAMMPS via Python through the LAMMPS library interface -you cannot also user the input script python command. - -
    Cannot evaporate atoms in atom_modify first group - -
    This is a restriction due to the way atoms are organized in -a list to enable the atom_modify first command. - -
    Cannot find create_bonds group ID - -
    Self-explanatory. - -
    Cannot find delete_bonds group ID - -
    Group ID used in the delete_bonds command does not exist. - -
    Cannot find specified group ID for core particles - -
    Self-explanatory. - -
    Cannot find specified group ID for shell particles - -
    Self-explanatory. - -
    Cannot have both pair_modify shift and tail set to yes - -
    These 2 options are contradictory. - -
    Cannot intersect groups using a dynamic group - -
    This operation is not allowed. - -
    Cannot mix molecular and molecule template atom styles - -
    Self-explanatory. - -
    Cannot open -reorder file - -
    Self-explanatory. - -
    Cannot open ADP potential file %s - -
    The specified ADP potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open AIREBO potential file %s - -
    The specified AIREBO potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open BOP potential file %s - -
    The specified BOP potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open COMB potential file %s - -
    The specified COMB potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open COMB3 lib.comb3 file - -
    The COMB3 library file cannot be opened. Check that the path and name -are correct. - -
    Cannot open COMB3 potential file %s - -
    The specified COMB3 potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open EAM potential file %s - -
    The specified EAM potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open EIM potential file %s - -
    The specified EIM potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open LCBOP potential file %s - -
    The specified LCBOP potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open MEAM potential file %s - -
    The specified MEAM potential file cannot be opened. Check that the -path and name are correct. - -
    Cannot open SNAP coefficient file %s - -
    The specified SNAP coefficient file cannot be opened. Check that the -path and name are correct. - -
    Cannot open SNAP parameter file %s - -
    The specified SNAP parameter file cannot be opened. Check that the -path and name are correct. - -
    Cannot open Stillinger-Weber potential file %s - -
    The specified SW potential file cannot be opened. Check that the path -and name are correct. - -
    Cannot open Tersoff potential file %s - -
    The specified potential file cannot be opened. Check that the path -and name are correct. - -
    Cannot open balance output file - -
    Self-explanatory. - -
    Cannot open coul/streitz potential file %s - -
    The specified coul/streitz potential file cannot be opened. Check -that the path and name are correct. - -
    Cannot open custom file - -
    Self-explanatory. - -
    Cannot open data file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open dir to search for restart file - -
    Using a "*" in the name of the restart file will open the current -directory to search for matching file names. - -
    Cannot open dump file - -
    The output file for the dump command cannot be opened. Check that the -path and name are correct. - -
    Cannot open dump file %s - -
    The output file for the dump command cannot be opened. Check that the -path and name are correct. - -
    Cannot open file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. If the file is a compressed file, also check that the gzip -executable can be found and run. - -
    Cannot open file variable file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix ave/chunk file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix ave/correlate file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix ave/histo file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix ave/spatial file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix ave/time file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix balance output file - -
    Self-explanatory. - -
    Cannot open fix poems file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix print file %s - -
    The output file generated by the fix print command cannot be opened - -
    Cannot open fix qeq parameter file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix qeq/comb file %s - -
    The output file for the fix qeq/combs command cannot be opened. -Check that the path and name are correct. - -
    Cannot open fix reax/bonds file %s - -
    The output file for the fix reax/bonds command cannot be opened. -Check that the path and name are correct. - -
    Cannot open fix rigid infile %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix rigid restart file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix rigid/small infile %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open fix tmd file %s - -
    The output file for the fix tmd command cannot be opened. Check that -the path and name are correct. - -
    Cannot open fix ttm file %s - -
    The output file for the fix ttm command cannot be opened. Check that -the path and name are correct. - -
    Cannot open gzipped file - -
    LAMMPS was compiled without support for reading and writing gzipped -files through a pipeline to the gzip program with -DLAMMPS_GZIP. - -
    Cannot open input script %s - -
    Self-explanatory. - -
    Cannot open log.cite file - -
    This file is created when you use some LAMMPS features, to indicate -what paper you should cite on behalf of those who implemented -the feature. Check that you have write priveleges into the directory -you are running in. - -
    Cannot open log.lammps for writing - -
    The default LAMMPS log file cannot be opened. Check that the -directory you are running in allows for files to be created. - -
    Cannot open logfile - -
    The LAMMPS log file named in a command-line argument cannot be opened. -Check that the path and name are correct. - -
    Cannot open logfile %s - -
    The LAMMPS log file specified in the input script cannot be opened. -Check that the path and name are correct. - -
    Cannot open molecule file %s - -
    The specified file cannot be opened. Check that the path and name are -correct. - -
    Cannot open nb3b/harmonic potential file %s - -
    The specified potential file cannot be opened. Check that the path -and name are correct. - -
    Cannot open pair_write file - -
    The specified output file for pair energies and forces cannot be -opened. Check that the path and name are correct. - -
    Cannot open print file %s - -
    Self-explanatory. - -
    Cannot open processors output file - -
    Self-explanatory. - -
    Cannot open restart file %s - -
    Self-explanatory. - -
    Cannot open restart file for reading - MPI error: %s - -
    This error was generated by MPI when reading/writing an MPI-IO restart -file. - -
    Cannot open restart file for writing - MPI error: %s - -
    This error was generated by MPI when reading/writing an MPI-IO restart -file. - -
    Cannot open screen file - -
    The screen file specified as a command-line argument cannot be -opened. Check that the directory you are running in allows for files -to be created. - -
    Cannot open universe log file - -
    For a multi-partition run, the master log file cannot be opened. -Check that the directory you are running in allows for files to be -created. - -
    Cannot open universe screen file - -
    For a multi-partition run, the master screen file cannot be opened. -Check that the directory you are running in allows for files to be -created. - -
    Cannot read from restart file - MPI error: %s - -
    This error was generated by MPI when reading/writing an MPI-IO restart -file. - -
    Cannot read_data add and merge - -
    These options are not yet supported. - -
    Cannot read_data after simulation box is defined - -
    The read_data command cannot be used after a read_data, -read_restart, or create_box command. - -
    Cannot read_restart after simulation box is defined - -
    The read_restart command cannot be used after a read_data, -read_restart, or create_box command. - -
    Cannot redefine variable as a different style - -
    An equal-style variable can be re-defined but only if it was -originally an equal-style variable. - -
    Cannot replicate 2d simulation in z dimension - -
    The replicate command cannot replicate a 2d simulation in the z -dimension. - -
    Cannot replicate with fixes that store atom quantities - -
    Either fixes are defined that create and store atom-based vectors or a -restart file was read which included atom-based vectors for fixes. -The replicate command cannot duplicate that information for new atoms. -You should use the replicate command before fixes are applied to the -system. - -
    Cannot reset timestep with a dynamic region defined - -
    Dynamic regions (see the region command) have a time dependence. -Thus you cannot change the timestep when one or more of these -are defined. - -
    Cannot reset timestep with a time-dependent fix defined - -
    You cannot reset the timestep when a fix that keeps track of elapsed -time is in place. - -
    Cannot run 2d simulation with nonperiodic Z dimension - -
    Use the boundary command to make the z dimension periodic in order to -run a 2d simulation. - -
    Cannot set bond topology types for atom style template - -
    The bond, angle, etc types cannot be changed for this atom style since -they are static settings in the molecule template files. - -
    Cannot set both respa pair and inner/middle/outer - -
    In the rRESPA integrator, you must compute pairwise potentials either -all together (pair), or in pieces (inner/middle/outer). You can't do -both. - -
    Cannot set dump_modify flush for dump xtc - -
    Self-explanatory. - -
    Cannot set mass for this atom style - -
    This atom style does not support mass settings for each atom type. -Instead they are defined on a per-atom basis in the data file. - -
    Cannot set meso_rho for this atom style - -
    Self-explanatory. - -
    Cannot set non-zero image flag for non-periodic dimension - -
    Self-explanatory. - -
    Cannot set non-zero z velocity for 2d simulation - -
    Self-explanatory. - -
    Cannot set quaternion for atom that has none - -
    Self-explanatory. - -
    Cannot set respa middle without inner/outer - -
    In the rRESPA integrator, you must define both a inner and outer -setting in order to use a middle setting. - -
    Cannot set restart file size - MPI error: %s - -
    This error was generated by MPI when reading/writing an MPI-IO restart -file. - -
    Cannot set temperature for fix rigid/nph - -
    The temp keyword cannot be specified. - -
    Cannot set theta for atom that is not a line - -
    Self-explanatory. - -
    Cannot set this attribute for this atom style - -
    The attribute being set does not exist for the defined atom style. - -
    Cannot set variable z velocity for 2d simulation - -
    Self-explanatory. - -
    Cannot skew triclinic box in z for 2d simulation - -
    Self-explanatory. - -
    Cannot subtract groups using a dynamic group - -
    This operation is not allowed. - -
    Cannot union groups using a dynamic group - -
    This operation is not allowed. - -
    Cannot use -cuda on and -kokkos on together - -
    This is not allowed since both packages can use GPUs. - -
    Cannot use -cuda on without USER-CUDA installed - -
    The USER-CUDA package must be installed via "make yes-user-cuda" -before LAMMPS is built. - -
    Cannot use -kokkos on without KOKKOS installed - -
    Self-explanatory. - -
    Cannot use -reorder after -partition - -
    Self-explanatory. See doc page discussion of command-line switches. - -
    Cannot use Ewald with 2d simulation - -
    The kspace style ewald cannot be used in 2d simulations. You can use -2d Ewald in a 3d simulation; see the kspace_modify command. - -
    Cannot use Ewald/disp solver on system with no charge, dipole, or LJ particles - -
    No atoms in system have a non-zero charge or dipole, or are LJ -particles. Change charges/dipoles or change options of the kspace -solver/pair style. - -
    Cannot use EwaldDisp with 2d simulation - -
    This is a current restriction of this command. - -
    Cannot use GPU package with USER-CUDA package enabled - -
    You cannot use both the GPU and USER-CUDA packages -together. Use one or the other. - -
    Cannot use Kokkos pair style with rRESPA inner/middle - -
    rRESPA inner/middle options are not yet supported by Kokkos. - -
    Cannot use NEB unless atom map exists - -
    Use the atom_modify command to create an atom map. - -
    Cannot use NEB with a single replica - -
    Self-explanatory. - -
    Cannot use NEB with atom_modify sort enabled - -
    This is current restriction for NEB implemented in LAMMPS. - -
    Cannot use PPPM with 2d simulation - -
    The kspace style pppm cannot be used in 2d simulations. You can use -2d PPPM in a 3d simulation; see the kspace_modify command. - -
    Cannot use PPPMDisp with 2d simulation - -
    The kspace style pppm/disp cannot be used in 2d simulations. You can -use 2d pppm/disp in a 3d simulation; see the kspace_modify command. - -
    Cannot use PRD with a changing box - -
    The current box dimensions are not copied between replicas - -
    Cannot use PRD with a time-dependent fix defined - -
    PRD alters the timestep in ways that will mess up these fixes. - -
    Cannot use PRD with a time-dependent region defined - -
    PRD alters the timestep in ways that will mess up these regions. - -
    Cannot use PRD with atom_modify sort enabled - -
    This is a current restriction of PRD. You must turn off sorting, -which is enabled by default, via the atom_modify command. - -
    Cannot use PRD with multi-processor replicas unless atom map exists - -
    Use the atom_modify command to create an atom map. - -
    Cannot use TAD unless atom map exists for NEB - -
    See atom_modify map command to set this. - -
    Cannot use TAD with a single replica for NEB - -
    NEB requires multiple replicas. - -
    Cannot use TAD with atom_modify sort enabled for NEB - -
    This is a current restriction of NEB. - -
    Cannot use a damped dynamics min style with fix box/relax - -
    This is a current restriction in LAMMPS. Use another minimizer -style. - -
    Cannot use a damped dynamics min style with per-atom DOF - -
    This is a current restriction in LAMMPS. Use another minimizer -style. - -
    Cannot use append/atoms in periodic dimension - -
    The boundary style of the face where atoms are added can not be of -type p (periodic). - -
    Cannot use atomfile-style variable unless atom map exists - -
    Self-explanatory. See the atom_modify command to create a map. - -
    Cannot use both com and bias with compute temp/chunk - -
    Self-explanatory. - -
    Cannot use chosen neighbor list style with buck/kk - -
    That style is not supported by Kokkos. - -
    Cannot use chosen neighbor list style with coul/cut/kk - -
    That style is not supported by Kokkos. - -
    Cannot use chosen neighbor list style with coul/dsf/kk - -
    That style is not supported by Kokkos. - -
    Cannot use chosen neighbor list style with coul/wolf/kk - -
    That style is not supported by Kokkos. - -
    Cannot use chosen neighbor list style with lj/cut/coul/cut/kk - -
    That style is not supported by Kokkos. - -
    Cannot use chosen neighbor list style with lj/cut/coul/long/kk - -
    That style is not supported by Kokkos. - -
    Cannot use chosen neighbor list style with lj/cut/kk - -
    That style is not supported by Kokkos. - -
    Cannot use chosen neighbor list style with pair eam/kk - -
    That style is not supported by Kokkos. - -
    Cannot use compute chunk/atom bin z for 2d model - -
    Self-explanatory. - -
    Cannot use compute cluster/atom unless atoms have IDs - -
    Atom IDs are used to identify clusters. - -
    Cannot use create_atoms rotate unless single style - -
    Self-explanatory. - -
    Cannot use create_bonds unless atoms have IDs - -
    This command requires a mapping from global atom IDs to local atoms, -but the atoms that have been defined have no IDs. - -
    Cannot use create_bonds with non-molecular system - -
    Self-explanatory. - -
    Cannot use cwiggle in variable formula between runs - -
    This is a function of elapsed time. - -
    Cannot use delete_atoms bond yes with atom_style template - -
    This is because the bonds for that atom style are hardwired in the -molecule template. - -
    Cannot use delete_atoms unless atoms have IDs - -
    Your atoms do not have IDs, so the delete_atoms command cannot be -used. - -
    Cannot use delete_bonds with non-molecular system - -
    Your choice of atom style does not have bonds. - -
    Cannot use dump_modify fileper without % in dump file name - -
    Self-explanatory. - -
    Cannot use dump_modify nfile without % in dump file name - -
    Self-explanatory. - -
    Cannot use dynamic group with fix adapt atom - -
    This is not yet supported. - -
    Cannot use fix TMD unless atom map exists - -
    Using this fix requires the ability to lookup an atom index, which is -provided by an atom map. An atom map does not exist (by default) for -non-molecular problems. Using the atom_modify map command will force -an atom map to be created. - -
    Cannot use fix ave/spatial z for 2 dimensional model - -
    Self-explanatory. - -
    Cannot use fix bond/break with non-molecular systems - -
    Only systems with bonds that can be changed can be used. Atom_style -template does not qualify. - -
    Cannot use fix bond/create with non-molecular systems - -
    Only systems with bonds that can be changed can be used. Atom_style -template does not qualify. - -
    Cannot use fix bond/swap with non-molecular systems - -
    Only systems with bonds that can be changed can be used. Atom_style -template does not qualify. - -
    Cannot use fix box/relax on a 2nd non-periodic dimension - -
    When specifying an off-diagonal pressure component, the 2nd of the two -dimensions must be periodic. E.g. if the xy component is specified, -then the y dimension must be periodic. - -
    Cannot use fix box/relax on a non-periodic dimension - -
    When specifying a diagonal pressure component, the dimension must be -periodic. - -
    Cannot use fix box/relax with both relaxation and scaling on a tilt factor - -
    When specifying scaling on a tilt factor component, that component can not -also be controlled by the barostat. E.g. if scalexy yes is specified and -also keyword tri or xy, this is wrong. - -
    Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension - -
    When specifying scaling on a tilt factor component, the 2nd of the two -dimensions must be periodic. E.g. if the xy component is specified, -then the y dimension must be periodic. - -
    Cannot use fix deform on a shrink-wrapped boundary - -
    The x, y, z options cannot be applied to shrink-wrapped -dimensions. - -
    Cannot use fix deform tilt on a shrink-wrapped 2nd dim - -
    This is because the shrink-wrapping will change the value -of the strain implied by the tilt factor. - -
    Cannot use fix deform trate on a box with zero tilt - -
    The trate style alters the current strain. - -
    Cannot use fix deposit rigid and not molecule - -
    Self-explanatory. - -
    Cannot use fix deposit rigid and shake - -
    These two attributes are conflicting. - -
    Cannot use fix deposit shake and not molecule - -
    Self-explanatory. - -
    Cannot use fix enforce2d with 3d simulation - -
    Self-explanatory. - -
    Cannot use fix gcmc in a 2d simulation - -
    Fix gcmc is set up to run in 3d only. No 2d simulations with fix gcmc -are allowed. - -
    Cannot use fix gcmc shake and not molecule - -
    Self-explanatory. - -
    Cannot use fix msst without per-type mass defined - -
    Self-explanatory. - -
    Cannot use fix npt and fix deform on same component of stress tensor - -
    This would be changing the same box dimension twice. - -
    Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension - -
    When specifying an off-diagonal pressure component, the 2nd of the two -dimensions must be periodic. E.g. if the xy component is specified, -then the y dimension must be periodic. - -
    Cannot use fix nvt/npt/nph on a non-periodic dimension - -
    When specifying a diagonal pressure component, the dimension must be -periodic. - -
    Cannot use fix nvt/npt/nph with both xy dynamics and xy scaling - -
    Self-explanatory. - -
    Cannot use fix nvt/npt/nph with both xz dynamics and xz scaling - -
    Self-explanatory. - -
    Cannot use fix nvt/npt/nph with both yz dynamics and yz scaling - -
    Self-explanatory. - -
    Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension - -
    The 2nd dimension in the barostatted tilt factor must be periodic. - -
    Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension - -
    The 2nd dimension in the barostatted tilt factor must be periodic. - -
    Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension - -
    The 2nd dimension in the barostatted tilt factor must be periodic. - -
    Cannot use fix pour rigid and not molecule - -
    Self-explanatory. - -
    Cannot use fix pour rigid and shake - -
    These two attributes are conflicting. - -
    Cannot use fix pour shake and not molecule - -
    Self-explanatory. - -
    Cannot use fix pour with triclinic box - -
    This option is not yet supported. - -
    Cannot use fix press/berendsen and fix deform on same component of stress tensor - -
    These commands both change the box size/shape, so you cannot use both -together. - -
    Cannot use fix press/berendsen on a non-periodic dimension - -
    Self-explanatory. - -
    Cannot use fix press/berendsen with triclinic box - -
    Self-explanatory. - -
    Cannot use fix reax/bonds without pair_style reax - -
    Self-explantory. - -
    Cannot use fix rigid npt/nph and fix deform on same component of stress tensor - -
    This would be changing the same box dimension twice. - -
    Cannot use fix rigid npt/nph on a non-periodic dimension - -
    When specifying a diagonal pressure component, the dimension must be -periodic. - -
    Cannot use fix rigid/small npt/nph on a non-periodic dimension - -
    When specifying a diagonal pressure component, the dimension must be -periodic. - -
    Cannot use fix shake with non-molecular system - -
    Your choice of atom style does not have bonds. - -
    Cannot use fix ttm with 2d simulation - -
    This is a current restriction of this fix due to the grid it creates. - -
    Cannot use fix ttm with triclinic box - -
    This is a current restriction of this fix due to the grid it creates. - -
    Cannot use fix tune/kspace without a kspace style - -
    Self-explanatory. - -
    Cannot use fix tune/kspace without a pair style - -
    This fix (tune/kspace) can only be used when a pair style has been specified. - -
    Cannot use fix wall in periodic dimension - -
    Self-explanatory. - -
    Cannot use fix wall zlo/zhi for a 2d simulation - -
    Self-explanatory. - -
    Cannot use fix wall/reflect in periodic dimension - -
    Self-explanatory. - -
    Cannot use fix wall/reflect zlo/zhi for a 2d simulation - -
    Self-explanatory. - -
    Cannot use fix wall/srd in periodic dimension - -
    Self-explanatory. - -
    Cannot use fix wall/srd more than once - -
    Nor is their a need to since multiple walls can be specified -in one command. - -
    Cannot use fix wall/srd without fix srd - -
    Self-explanatory. - -
    Cannot use fix wall/srd zlo/zhi for a 2d simulation - -
    Self-explanatory. - -
    Cannot use fix_deposit unless atoms have IDs - -
    Self-explanatory. - -
    Cannot use fix_pour unless atoms have IDs - -
    Self-explanatory. - -
    Cannot use include command within an if command - -
    Self-explanatory. - -
    Cannot use lines with fix srd unless overlap is set - -
    This is because line segements are connected to each other. - -
    Cannot use multiple fix wall commands with pair brownian - -
    Self-explanatory. - -
    Cannot use multiple fix wall commands with pair lubricate - -
    Self-explanatory. - -
    Cannot use multiple fix wall commands with pair lubricate/poly - -
    Self-explanatory. - -
    Cannot use multiple fix wall commands with pair lubricateU - -
    Self-explanatory. - -
    Cannot use neigh_modify exclude with GPU neighbor builds - -
    This is a current limitation of the GPU implementation -in LAMMPS. - -
    Cannot use neighbor bins - box size << cutoff - -
    Too many neighbor bins will be created. This typically happens when -the simulation box is very small in some dimension, compared to the -neighbor cutoff. Use the "nsq" style instead of "bin" style. - -
    Cannot use newton pair with beck/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with born/coul/long/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with born/coul/wolf/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with born/gpu pair style - -
    Self-explantory. - -
    Cannot use newton pair with buck/coul/cut/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with buck/coul/long/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with buck/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with colloid/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with coul/cut/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with coul/debye/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with coul/dsf/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with coul/long/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with dipole/cut/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with dpd/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with dpd/tstat/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with eam/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with gauss/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with gayberne/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/charmm/coul/long/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/class2/coul/long/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/class2/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/cut/coul/cut/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/cut/coul/debye/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/cut/coul/dsf/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/cut/coul/long/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/cut/coul/msm/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/cut/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/expand/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj/gromacs/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with lj96/cut/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with mie/cut/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with morse/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with resquared/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with soft/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with table/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with yukawa/colloid/gpu pair style - -
    Self-explanatory. - -
    Cannot use newton pair with yukawa/gpu pair style - -
    Self-explanatory. - -
    Cannot use non-zero forces in an energy minimization - -
    Fix setforce cannot be used in this manner. Use fix addforce -instead. - -
    Cannot use non-zero z offset in read_data for 2d simulation - -
    The offset option is not yet supported. - -
    Cannot use nonperiodic boundares with fix ttm - -
    This fix requires a fully periodic simulation box. - -
    Cannot use nonperiodic boundaries with Ewald - -
    For kspace style ewald, all 3 dimensions must have periodic boundaries -unless you use the kspace_modify command to define a 2d slab with a -non-periodic z dimension. - -
    Cannot use nonperiodic boundaries with EwaldDisp - -
    For kspace style ewald/disp, all 3 dimensions must have periodic -boundaries unless you use the kspace_modify command to define a 2d -slab with a non-periodic z dimension. - -
    Cannot use nonperiodic boundaries with PPPM - -
    For kspace style pppm, all 3 dimensions must have periodic boundaries -unless you use the kspace_modify command to define a 2d slab with a -non-periodic z dimension. - -
    Cannot use nonperiodic boundaries with PPPMDisp - -
    For kspace style pppm/disp, all 3 dimensions must have periodic -boundaries unless you use the kspace_modify command to define a 2d -slab with a non-periodic z dimension. - -
    Cannot use order greater than 8 with pppm/gpu. - -
    Self-explanatory. - -
    Cannot use package gpu neigh yes with triclinic box - -
    This is a current restriction in LAMMPS. - -
    Cannot use pair hybrid with GPU neighbor list builds - -
    Neighbor list builds must be done on the CPU for this pair style. - -
    Cannot use pair tail corrections with 2d simulations - -
    The correction factors are only currently defined for 3d systems. - -
    Cannot use processors part command without using partitions - -
    See the command-line -partition switch. - -
    Cannot use ramp in variable formula between runs - -
    This is because the ramp() function is time dependent. - -
    Cannot use region INF or EDGE when box does not exist - -
    Regions that extend to the box boundaries can only be used after the -create_box command has been used. - -
    Cannot use set atom with no atom IDs defined - -
    Atom IDs are not defined, so they cannot be used to identify an atom. - -
    Cannot use set mol with no molecule IDs defined - -
    Self-explanatory. - -
    Cannot use swiggle in variable formula between runs - -
    This is a function of elapsed time. - -
    Cannot use tris with fix srd unless overlap is set - -
    This is because triangles are connected to each other. - -
    Cannot use variable energy with constant efield in fix efield - -
    LAMMPS computes the energy itself when the E-field is constant. - -
    Cannot use variable energy with constant force in fix addforce - -
    This is because for constant force, LAMMPS can compute the change -in energy directly. - -
    Cannot use variable every setting for dump dcd - -
    The format of DCD dump files requires snapshots be output -at a constant frequency. - -
    Cannot use variable every setting for dump xtc - -
    The format of this file requires snapshots at regular intervals. - -
    Cannot use vdisplace in variable formula between runs - -
    This is a function of elapsed time. - -
    Cannot use velocity bias command without temp keyword - -
    Self-explanatory. - -
    Cannot use velocity create loop all unless atoms have IDs - -
    Atoms in the simulation to do not have IDs, so this style -of velocity creation cannot be performed. - -
    Cannot use wall in periodic dimension - -
    Self-explanatory. - -
    Cannot use write_restart fileper without % in restart file name - -
    Self-explanatory. - -
    Cannot use write_restart nfile without % in restart file name - -
    Self-explanatory. - -
    Cannot wiggle and shear fix wall/gran - -
    Cannot specify both options at the same time. - -
    Cannot write to restart file - MPI error: %s - -
    This error was generated by MPI when reading/writing an MPI-IO restart -file. - -
    Cannot yet use KSpace solver with grid with comm style tiled - -
    This is current restriction in LAMMPS. - -
    Cannot yet use comm_style tiled with multi-mode comm - -
    Self-explanatory. - -
    Cannot yet use comm_style tiled with triclinic box - -
    Self-explanatory. - -
    Cannot yet use fix bond/break with this improper style - -
    This is a current restriction in LAMMPS. - -
    Cannot yet use fix bond/create with this improper style - -
    This is a current restriction in LAMMPS. - -
    Cannot zero Langevin force of 0 atoms - -
    The group has zero atoms, so you cannot request its force -be zeroed. - -
    Cannot zero gld force for zero atoms - -
    There are no atoms currently in the group. - -
    Cannot zero momentum of no atoms - -
    Self-explanatory. - -
    Change_box command before simulation box is defined - -
    Self-explanatory. - -
    Change_box volume used incorrectly - -
    The "dim volume" option must be used immediately following one or two -settings for "dim1 ..." (and optionally "dim2 ...") and must be for a -different dimension, i.e. dim != dim1 and dim != dim2. - -
    Chunk/atom compute does not exist for compute angmom/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute com/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute gyration/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute inertia/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute msd/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute omega/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute property/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute temp/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute torque/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for compute vcm/chunk - -
    Self-explanatory. - -
    Chunk/atom compute does not exist for fix ave/chunk - -
    Self-explanatory. - -
    Comm tiled invalid index in box drop brick - -
    Internal error check in comm_style tiled which should not occur. -Contact the developers. - -
    Comm tiled mis-match in box drop brick - -
    Internal error check in comm_style tiled which should not occur. -Contact the developers. - -
    Comm_modify group != atom_modify first group - -
    Self-explanatory. - -
    Communication cutoff for comm_style tiled cannot exceed periodic box length - -
    Self-explanatory. - -
    Communication cutoff too small for SNAP micro load balancing - -
    This can happen if you change the neighbor skin after your pair_style -command or if your box dimensions grow during a run. You can set the -cutoff explicitly via the comm_modify cutoff command. - -
    Compute %s does not allow use of dynamic group - -
    Dynamic groups have not yet been enabled for this compute. - -
    Compute ID for compute chunk/atom does not exist - -
    Self-explanatory. - -
    Compute ID for compute reduce does not exist - -
    Self-explanatory. - -
    Compute ID for compute slice does not exist - -
    Self-explanatory. - -
    Compute ID for fix ave/atom does not exist - -
    Self-explanatory. - -
    Compute ID for fix ave/chunk does not exist - -
    Self-explanatory. - -
    Compute ID for fix ave/correlate does not exist - -
    Self-explanatory. - -
    Compute ID for fix ave/histo does not exist - -
    Self-explanatory. - -
    Compute ID for fix ave/spatial does not exist - -
    Self-explanatory. - -
    Compute ID for fix ave/time does not exist - -
    Self-explanatory. - -
    Compute ID for fix store/state does not exist - -
    Self-explanatory. - -
    Compute ID for fix vector does not exist - -
    Self-explanatory. - -
    Compute ID must be alphanumeric or underscore characters - -
    Self-explanatory. - -
    Compute angle/local used when angles are not allowed - -
    The atom style does not support angles. - -
    Compute angmom/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute body/local requires atom style body - -
    Self-explanatory. - -
    Compute bond/local used when bonds are not allowed - -
    The atom style does not support bonds. - -
    Compute centro/atom requires a pair style be defined - -
    This is because the computation of the centro-symmetry values -uses a pairwise neighbor list. - -
    Compute chunk/atom compute array is accessed out-of-range - -
    The index for the array is out of bounds. - -
    Compute chunk/atom compute does not calculate a per-atom array - -
    Self-explanatory. - -
    Compute chunk/atom compute does not calculate a per-atom vector - -
    Self-explanatory. - -
    Compute chunk/atom compute does not calculate per-atom values - -
    Self-explanatory. - -
    Compute chunk/atom fix array is accessed out-of-range - -
    the index for the array is out of bounds. - -
    Compute chunk/atom fix does not calculate a per-atom array - -
    Self-explanatory. - -
    Compute chunk/atom fix does not calculate a per-atom vector - -
    Self-explanatory. - -
    Compute chunk/atom fix does not calculate per-atom values - -
    Self-explanatory. - -
    Compute chunk/atom for triclinic boxes requires units reduced - -
    Self-explanatory. - -
    Compute chunk/atom ids once but nchunk is not once - -
    You cannot assign chunks IDs to atom permanently if the number of -chunks may change. - -
    Compute chunk/atom molecule for non-molecular system - -
    Self-explanatory. - -
    Compute chunk/atom stores no IDs for compute property/chunk - -
    It will only store IDs if its compress option is enabled. - -
    Compute chunk/atom stores no coord1 for compute property/chunk - -
    Only certain binning options for comptue chunk/atom store coordinates. - -
    Compute chunk/atom stores no coord2 for compute property/chunk - -
    Only certain binning options for comptue chunk/atom store coordinates. - -
    Compute chunk/atom stores no coord3 for compute property/chunk - -
    Only certain binning options for comptue chunk/atom store coordinates. - -
    Compute chunk/atom variable is not atom-style variable - -
    Self-explanatory. - -
    Compute chunk/atom without bins cannot use discard mixed - -
    That discard option only applies to the binning styles. - -
    Compute cluster/atom cutoff is longer than pairwise cutoff - -
    Cannot identify clusters beyond cutoff. - -
    Compute cluster/atom requires a pair style be defined - -
    This is so that the pair style defines a cutoff distance which -is used to find clusters. - -
    Compute cna/atom cutoff is longer than pairwise cutoff - -
    Self-explantory. - -
    Compute cna/atom requires a pair style be defined - -
    Self-explantory. - -
    Compute com/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute contact/atom requires a pair style be defined - -
    Self-explantory. - -
    Compute contact/atom requires atom style sphere - -
    Self-explanatory. - -
    Compute coord/atom cutoff is longer than pairwise cutoff - -
    Cannot compute coordination at distances longer than the pair cutoff, -since those atoms are not in the neighbor list. - -
    Compute coord/atom requires a pair style be defined - -
    Self-explantory. - -
    Compute damage/atom requires peridynamic potential - -
    Damage is a Peridynamic-specific metric. It requires you -to be running a Peridynamics simulation. - -
    Compute dihedral/local used when dihedrals are not allowed - -
    The atom style does not support dihedrals. - -
    Compute dilatation/atom cannot be used with this pair style - -
    Self-explanatory. - -
    Compute dilatation/atom requires Peridynamic pair style - -
    Self-explanatory. - -
    Compute does not allow an extra compute or fix to be reset - -
    This is an internal LAMMPS error. Please report it to the -developers. - -
    Compute erotate/asphere requires atom style ellipsoid or line or tri - -
    Self-explanatory. - -
    Compute erotate/asphere requires extended particles - -
    This compute cannot be used with point paritlces. - -
    Compute erotate/rigid with non-rigid fix-ID - -
    Self-explanatory. - -
    Compute erotate/sphere requires atom style sphere - -
    Self-explanatory. - -
    Compute erotate/sphere/atom requires atom style sphere - -
    Self-explanatory. - -
    Compute event/displace has invalid fix event assigned - -
    This is an internal LAMMPS error. Please report it to the -developers. - -
    Compute group/group group ID does not exist - -
    Self-explanatory. - -
    Compute gyration/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute heat/flux compute ID does not compute ke/atom - -
    Self-explanatory. - -
    Compute heat/flux compute ID does not compute pe/atom - -
    Self-explanatory. - -
    Compute heat/flux compute ID does not compute stress/atom - -
    Self-explanatory. - -
    Compute improper/local used when impropers are not allowed - -
    The atom style does not support impropers. - -
    Compute inertia/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute ke/rigid with non-rigid fix-ID - -
    Self-explanatory. - -
    Compute msd/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute msd/chunk nchunk is not static - -
    This is required because the MSD cannot be computed consistently if -the number of chunks is changing. Compute chunk/atom allows setting -nchunk to be static. - -
    Compute nve/asphere requires atom style ellipsoid - -
    Self-explanatory. - -
    Compute nvt/nph/npt asphere requires atom style ellipsoid - -
    Self-explanatory. - -
    Compute omega/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute pair must use group all - -
    Pair styles accumlate energy on all atoms. - -
    Compute pe must use group all - -
    Energies computed by potentials (pair, bond, etc) are computed on all -atoms. - -
    Compute plasticity/atom cannot be used with this pair style - -
    Self-explanatory. - -
    Compute plasticity/atom requires Peridynamic pair style - -
    Self-explanatory. - -
    Compute pressure must use group all - -
    Virial contributions computed by potentials (pair, bond, etc) are -computed on all atoms. - -
    Compute pressure requires temperature ID to include kinetic energy - -
    The keflag cannot be used unless a temperature compute is provided. - -
    Compute pressure temperature ID does not compute temperature - -
    The compute ID assigned to a pressure computation must compute -temperature. - -
    Compute property/atom floating point vector does not exist - -
    The command is accessing a vector added by the fix property/atom -command, that does not exist. - -
    Compute property/atom for atom property that isn't allocated - -
    Self-explanatory. - -
    Compute property/atom integer vector does not exist - -
    The command is accessing a vector added by the fix property/atom -command, that does not exist. - -
    Compute property/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute property/local cannot use these inputs together - -
    Only inputs that generate the same number of datums can be used -togther. E.g. bond and angle quantities cannot be mixed. - -
    Compute property/local does not (yet) work with atom_style template - -
    Self-explanatory. - -
    Compute property/local for property that isn't allocated - -
    Self-explanatory. - -
    Compute rdf requires a pair style be defined - -
    Self-explanatory. - -
    Compute reduce compute array is accessed out-of-range - -
    An index for the array is out of bounds. - -
    Compute reduce compute calculates global values - -
    A compute that calculates peratom or local values is required. - -
    Compute reduce compute does not calculate a local array - -
    Self-explanatory. - -
    Compute reduce compute does not calculate a local vector - -
    Self-explanatory. - -
    Compute reduce compute does not calculate a per-atom array - -
    Self-explanatory. - -
    Compute reduce compute does not calculate a per-atom vector - -
    Self-explanatory. - -
    Compute reduce fix array is accessed out-of-range - -
    An index for the array is out of bounds. - -
    Compute reduce fix calculates global values - -
    A fix that calculates peratom or local values is required. - -
    Compute reduce fix does not calculate a local array - -
    Self-explanatory. - -
    Compute reduce fix does not calculate a local vector - -
    Self-explanatory. - -
    Compute reduce fix does not calculate a per-atom array - -
    Self-explanatory. - -
    Compute reduce fix does not calculate a per-atom vector - -
    Self-explanatory. - -
    Compute reduce replace requires min or max mode - -
    Self-explanatory. - -
    Compute reduce variable is not atom-style variable - -
    Self-explanatory. - -
    Compute slice compute array is accessed out-of-range - -
    An index for the array is out of bounds. - -
    Compute slice compute does not calculate a global array - -
    Self-explanatory. - -
    Compute slice compute does not calculate a global vector - -
    Self-explanatory. - -
    Compute slice compute does not calculate global vector or array - -
    Self-explanatory. - -
    Compute slice compute vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Compute slice fix array is accessed out-of-range - -
    An index for the array is out of bounds. - -
    Compute slice fix does not calculate a global array - -
    Self-explanatory. - -
    Compute slice fix does not calculate a global vector - -
    Self-explanatory. - -
    Compute slice fix does not calculate global vector or array - -
    Self-explanatory. - -
    Compute slice fix vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Compute sna/atom cutoff is longer than pairwise cutoff - -
    Self-explanatory. - -
    Compute sna/atom requires a pair style be defined - -
    Self-explanatory. - -
    Compute snad/atom cutoff is longer than pairwise cutoff - -
    Self-explanatory. - -
    Compute snad/atom requires a pair style be defined - -
    Self-explanatory. - -
    Compute snav/atom cutoff is longer than pairwise cutoff - -
    Self-explanatory. - -
    Compute snav/atom requires a pair style be defined - -
    Self-explanatory. - -
    Compute stress/atom temperature ID does not compute temperature - -
    The specified compute must compute temperature. - -
    Compute temp/asphere requires atom style ellipsoid - -
    Self-explanatory. - -
    Compute temp/asphere requires extended particles - -
    This compute cannot be used with point paritlces. - -
    Compute temp/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute temp/cs requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Compute temp/cs used when bonds are not allowed - -
    This compute only works on pairs of bonded particles. - -
    Compute temp/partial cannot use vz for 2d systemx - -
    Self-explanatory. - -
    Compute temp/profile cannot bin z for 2d systems - -
    Self-explanatory. - -
    Compute temp/profile cannot use vz for 2d systemx - -
    Self-explanatory. - -
    Compute temp/sphere requires atom style sphere - -
    Self-explanatory. - -
    Compute ti kspace style does not exist - -
    Self-explanatory. - -
    Compute ti pair style does not exist - -
    Self-explanatory. - -
    Compute ti tail when pair style does not compute tail corrections - -
    Self-explanatory. - -
    Compute torque/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Compute used in dump between runs is not current - -
    The compute was not invoked on the current timestep, therefore it -cannot be used in a dump between runs. - -
    Compute used in variable between runs is not current - -
    Computes cannot be invoked by a variable in between runs. Thus they -must have been evaluated on the last timestep of the previous run in -order for their value(s) to be accessed. See the doc page for the -variable command for more info. - -
    Compute used in variable thermo keyword between runs is not current - -
    Some thermo keywords rely on a compute to calculate their value(s). -Computes cannot be invoked by a variable in between runs. Thus they -must have been evaluated on the last timestep of the previous run in -order for their value(s) to be accessed. See the doc page for the -variable command for more info. - -
    Compute vcm/chunk does not use chunk/atom compute - -
    The style of the specified compute is not chunk/atom. - -
    Computed temperature for fix temp/berendsen cannot be 0.0 - -
    Self-explanatory. - -
    Computed temperature for fix temp/rescale cannot be 0.0 - -
    Cannot rescale the temperature to a new value if the current -temperature is 0.0. - -
    Core/shell partner atom not found - -
    Could not find one of the atoms in the bond pair. - -
    Core/shell partners were not all found - -
    Could not find or more atoms in the bond pairs. - -
    Could not adjust g_ewald_6 - -
    The Newton-Raphson solver failed to converge to a good value for -g_ewald. This error should not occur for typical problems. Please -send an email to the developers. - -
    Could not compute g_ewald - -
    The Newton-Raphson solver failed to converge to a good value for -g_ewald. This error should not occur for typical problems. Please -send an email to the developers. - -
    Could not compute grid size - -
    The code is unable to compute a grid size consistent with the desired -accuracy. This error should not occur for typical problems. Please -send an email to the developers. - -
    Could not compute grid size for Coulomb interaction - -
    The code is unable to compute a grid size consistent with the desired -accuracy. This error should not occur for typical problems. Please -send an email to the developers. - -
    Could not compute grid size for Dispersion - -
    The code is unable to compute a grid size consistent with the desired -accuracy. This error should not occur for typical problems. Please -send an email to the developers. - -
    Could not create 3d FFT plan - -
    The FFT setup for the PPPM solver failed, typically due -to lack of memory. This is an unusual error. Check the -size of the FFT grid you are requesting. - -
    Could not create 3d grid of processors - -
    The specified constraints did not allow a Px by Py by Pz grid to be -created where Px * Py * Pz = P = total number of processors. - -
    Could not create 3d remap plan - -
    The FFT setup in pppm failed. - -
    Could not create Python function arguments - -
    This is an internal Python error, possibly because the number -of inputs to the function is too large. - -
    Could not create numa grid of processors - -
    The specified constraints did not allow this style of grid to be -created. Usually this is because the total processor count is not a -multiple of the cores/node or the user specified processor count is > -1 in one of the dimensions. - -
    Could not create twolevel 3d grid of processors - -
    The specified constraints did not allow this style of grid to be -created. - -
    Could not evaluate Python function input variable - -
    Self-explanatory. - -
    Could not find Python function - -
    The provided Python code was run successfully, but it not -define a callable function with the required name. - -
    Could not find atom_modify first group ID - -
    Self-explanatory. - -
    Could not find change_box group ID - -
    Group ID used in the change_box command does not exist. - -
    Could not find compute ID for PRD - -
    Self-explanatory. - -
    Could not find compute ID for TAD - -
    Self-explanatory. - -
    Could not find compute ID for temperature bias - -
    Self-explanatory. - -
    Could not find compute ID to delete - -
    Self-explanatory. - -
    Could not find compute displace/atom fix ID - -
    Self-explanatory. - -
    Could not find compute event/displace fix ID - -
    Self-explanatory. - -
    Could not find compute group ID - -
    Self-explanatory. - -
    Could not find compute heat/flux compute ID - -
    Self-explanatory. - -
    Could not find compute msd fix ID - -
    Self-explanatory. - -
    Could not find compute pressure temperature ID - -
    The compute ID for calculating temperature does not exist. - -
    Could not find compute stress/atom temperature ID - -
    Self-explanatory. - -
    Could not find compute vacf fix ID - -
    Self-explanatory. - -
    Could not find compute/voronoi surface group ID - -
    Self-explanatory. - -
    Could not find compute_modify ID - -
    Self-explanatory. - -
    Could not find custom per-atom property ID - -
    Self-explanatory. - -
    Could not find delete_atoms group ID - -
    Group ID used in the delete_atoms command does not exist. - -
    Could not find delete_atoms region ID - -
    Region ID used in the delete_atoms command does not exist. - -
    Could not find displace_atoms group ID - -
    Group ID used in the displace_atoms command does not exist. - -
    Could not find dump custom compute ID - -
    Self-explanatory. - -
    Could not find dump custom fix ID - -
    Self-explanatory. - -
    Could not find dump custom variable name - -
    Self-explanatory. - -
    Could not find dump group ID - -
    A group ID used in the dump command does not exist. - -
    Could not find dump local compute ID - -
    Self-explanatory. - -
    Could not find dump local fix ID - -
    Self-explanatory. - -
    Could not find dump modify compute ID - -
    Self-explanatory. - -
    Could not find dump modify custom atom floating point property ID - -
    Self-explanatory. - -
    Could not find dump modify custom atom integer property ID - -
    Self-explanatory. - -
    Could not find dump modify fix ID - -
    Self-explanatory. - -
    Could not find dump modify variable name - -
    Self-explanatory. - -
    Could not find fix ID to delete - -
    Self-explanatory. - -
    Could not find fix adapt storage fix ID - -
    This should not happen unless you explicitly deleted -a secondary fix that fix adapt created internally. - -
    Could not find fix gcmc exclusion group ID - -
    Self-explanatory. - -
    Could not find fix gcmc rotation group ID - -
    Self-explanatory. - -
    Could not find fix group ID - -
    A group ID used in the fix command does not exist. - -
    Could not find fix msst compute ID - -
    Self-explanatory. - -
    Could not find fix poems group ID - -
    A group ID used in the fix poems command does not exist. - -
    Could not find fix recenter group ID - -
    A group ID used in the fix recenter command does not exist. - -
    Could not find fix rigid group ID - -
    A group ID used in the fix rigid command does not exist. - -
    Could not find fix srd group ID - -
    Self-explanatory. - -
    Could not find fix_modify ID - -
    A fix ID used in the fix_modify command does not exist. - -
    Could not find fix_modify pressure ID - -
    The compute ID for computing pressure does not exist. - -
    Could not find fix_modify temperature ID - -
    The compute ID for computing temperature does not exist. - -
    Could not find group clear group ID - -
    Self-explanatory. - -
    Could not find group delete group ID - -
    Self-explanatory. - -
    Could not find set group ID - -
    Group ID specified in set command does not exist. - -
    Could not find thermo compute ID - -
    Compute ID specified in thermo_style command does not exist. - -
    Could not find thermo custom compute ID - -
    The compute ID needed by thermo style custom to compute a requested -quantity does not exist. - -
    Could not find thermo custom fix ID - -
    The fix ID needed by thermo style custom to compute a requested -quantity does not exist. - -
    Could not find thermo custom variable name - -
    Self-explanatory. - -
    Could not find thermo fix ID - -
    Fix ID specified in thermo_style command does not exist. - -
    Could not find thermo variable name - -
    Self-explanatory. - -
    Could not find thermo_modify pressure ID - -
    The compute ID needed by thermo style custom to compute pressure does -not exist. - -
    Could not find thermo_modify temperature ID - -
    The compute ID needed by thermo style custom to compute temperature does -not exist. - -
    Could not find undump ID - -
    A dump ID used in the undump command does not exist. - -
    Could not find velocity group ID - -
    A group ID used in the velocity command does not exist. - -
    Could not find velocity temperature ID - -
    The compute ID needed by the velocity command to compute temperature -does not exist. - -
    Could not find/initialize a specified accelerator device - -
    Could not initialize at least one of the devices specified for the gpu -package - -
    Could not grab element entry from EIM potential file - -
    Self-explanatory - -
    Could not grab global entry from EIM potential file - -
    Self-explanatory. - -
    Could not grab pair entry from EIM potential file - -
    Self-explanatory. - -
    Could not initialize embedded Python - -
    The main module in Python was not accessible. - -
    Could not open Python file - -
    The specified file of Python code cannot be opened. Check that the -path and name are correct. - -
    Could not process Python file - -
    The Python code in the specified file was not run sucessfully by -Python, probably due to errors in the Python code. - -
    Could not process Python string - -
    The Python code in the here string was not run sucessfully by Python, -probably due to errors in the Python code. - -
    Coulomb PPPMDisp order has been reduced below minorder - -
    The default minimum order is 2. This can be reset by the -kspace_modify minorder command. - -
    Coulomb cut not supported in pair_style buck/long/coul/coul - -
    Must use long-range Coulombic interactions. - -
    Coulomb cut not supported in pair_style lj/long/coul/long - -
    Must use long-range Coulombic interactions. - -
    Coulomb cut not supported in pair_style lj/long/tip4p/long - -
    Must use long-range Coulombic interactions. - -
    Coulomb cutoffs of pair hybrid sub-styles do not match - -
    If using a Kspace solver, all Coulomb cutoffs of long pair styles must -be the same. - -
    Coulombic cut not supported in pair_style lj/long/dipole/long - -
    Must use long-range Coulombic interactions. - -
    Cound not find dump_modify ID - -
    Self-explanatory. - -
    Create_atoms command before simulation box is defined - -
    The create_atoms command cannot be used before a read_data, -read_restart, or create_box command. - -
    Create_atoms molecule has atom IDs, but system does not - -
    The atom_style id command can be used to force atom IDs to be stored. - -
    Create_atoms molecule must have atom types - -
    The defined molecule does not specify atom types. - -
    Create_atoms molecule must have coordinates - -
    The defined molecule does not specify coordinates. - -
    Create_atoms region ID does not exist - -
    A region ID used in the create_atoms command does not exist. - -
    Create_bonds command before simulation box is defined - -
    Self-explanatory. - -
    Create_bonds command requires no kspace_style be defined - -
    This is so that atom pairs that are already bonded to not appear -in the neighbor list. - -
    Create_bonds command requires special_bonds 1-2 weights be 0.0 - -
    This is so that atom pairs that are already bonded to not appear in -the neighbor list. - -
    Create_bonds max distance > neighbor cutoff - -
    Can only create bonds for atom pairs that will be in neighbor list. - -
    Create_bonds requires a pair style be defined - -
    Self-explanatory. - -
    Create_box region ID does not exist - -
    Self-explanatory. - -
    Create_box region does not support a bounding box - -
    Not all regions represent bounded volumes. You cannot use -such a region with the create_box command. - -
    Custom floating point vector for fix store/state does not exist - -
    The command is accessing a vector added by the fix property/atom -command, that does not exist. - -
    Custom integer vector for fix store/state does not exist - -
    The command is accessing a vector added by the fix property/atom -command, that does not exist. - -
    Custom per-atom property ID is not floating point - -
    Self-explanatory. - -
    Custom per-atom property ID is not integer - -
    Self-explanatory. - -
    Cut-offs missing in pair_style lj/long/dipole/long - -
    Self-explanatory. - -
    Cutoffs missing in pair_style buck/long/coul/long - -
    Self-exlanatory. - -
    Cutoffs missing in pair_style lj/long/coul/long - -
    Self-explanatory. - -
    Cyclic loop in joint connections - -
    Fix poems cannot (yet) work with coupled bodies whose joints connect -the bodies in a ring (or cycle). - -
    Degenerate lattice primitive vectors - -
    Invalid set of 3 lattice vectors for lattice command. - -
    Delete region ID does not exist - -
    Self-explanatory. - -
    Delete_atoms command before simulation box is defined - -
    The delete_atoms command cannot be used before a read_data, -read_restart, or create_box command. - -
    Delete_atoms cutoff > max neighbor cutoff - -
    Can only delete atoms in atom pairs that will be in neighbor list. - -
    Delete_atoms requires a pair style be defined - -
    This is because atom deletion within a cutoff uses a pairwise -neighbor list. - -
    Delete_bonds command before simulation box is defined - -
    The delete_bonds command cannot be used before a read_data, -read_restart, or create_box command. - -
    Delete_bonds command with no atoms existing - -
    No atoms are yet defined so the delete_bonds command cannot be used. - -
    Delta_mu not allowed when not using semi-grand in fix atom/swap command - -
    Self-explanatory. - -
    Deposition region extends outside simulation box - -
    Self-explanatory. - -
    Did not assign all atoms correctly - -
    Atoms read in from a data file were not assigned correctly to -processors. This is likely due to some atom coordinates being -outside a non-periodic simulation box. - -
    Did not assign all restart atoms correctly - -
    Atoms read in from the restart file were not assigned correctly to -processors. This is likely due to some atom coordinates being outside -a non-periodic simulation box. Normally this should not happen. You -may wish to use the "remap" option on the read_restart command to see -if this helps. - -
    Did not find all elements in MEAM library file - -
    The requested elements were not found in the MEAM file. - -
    Did not find fix shake partner info - -
    Could not find bond partners implied by fix shake command. This error -can be triggered if the delete_bonds command was used before fix -shake, and it removed bonds without resetting the 1-2, 1-3, 1-4 -weighting list via the special keyword. - -
    Did not find keyword in table file - -
    Keyword used in pair_coeff command was not found in table file. - -
    Did not set pressure for fix rigid/nph - -
    The press keyword must be specified. - -
    Did not set temp for fix rigid/nvt/small - -
    Self-explanatory. - -
    Did not set temp or press for fix rigid/npt/small - -
    Self-explanatory. - -
    Did not set temperature for fix rigid/nvt - -
    The temp keyword must be specified. - -
    Did not set temperature or pressure for fix rigid/npt - -
    The temp and press keywords must be specified. - -
    Dihedral atom missing in delete_bonds - -
    The delete_bonds command cannot find one or more atoms in a particular -dihedral on a particular processor. The pairwise cutoff is too short -or the atoms are too far apart to make a valid dihedral. - -
    Dihedral atom missing in set command - -
    The set command cannot find one or more atoms in a particular dihedral -on a particular processor. The pairwise cutoff is too short or the -atoms are too far apart to make a valid dihedral. - -
    Dihedral atoms %d %d %d %d missing on proc %d at step %ld - -
    One or more of 4 atoms needed to compute a particular dihedral are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the dihedral has blown apart and an atom is -too far away. - -
    Dihedral atoms missing on proc %d at step %ld - -
    One or more of 4 atoms needed to compute a particular dihedral are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the dihedral has blown apart and an atom is -too far away. - -
    Dihedral charmm is incompatible with Pair style - -
    Dihedral style charmm must be used with a pair style charmm -in order for the 1-4 epsilon/sigma parameters to be defined. - -
    Dihedral coeff for hybrid has invalid style - -
    Dihedral style hybrid uses another dihedral style as one of its -coefficients. The dihedral style used in the dihedral_coeff command -or read from a restart file is not recognized. - -
    Dihedral coeffs are not set - -
    No dihedral coefficients have been assigned in the data file or via -the dihedral_coeff command. - -
    Dihedral style hybrid cannot have hybrid as an argument - -
    Self-explanatory. - -
    Dihedral style hybrid cannot have none as an argument - -
    Self-explanatory. - -
    Dihedral style hybrid cannot use same dihedral style twice - -
    Self-explanatory. - -
    Dihedral/improper extent > half of periodic box length - -
    This error was detected by the neigh_modify check yes setting. It is -an error because the dihedral atoms are so far apart it is ambiguous -how it should be defined. - -
    Dihedral_coeff command before dihedral_style is defined - -
    Coefficients cannot be set in the data file or via the dihedral_coeff -command until an dihedral_style has been assigned. - -
    Dihedral_coeff command before simulation box is defined - -
    The dihedral_coeff command cannot be used before a read_data, -read_restart, or create_box command. - -
    Dihedral_coeff command when no dihedrals allowed - -
    The chosen atom style does not allow for dihedrals to be defined. - -
    Dihedral_style command when no dihedrals allowed - -
    The chosen atom style does not allow for dihedrals to be defined. - -
    Dihedrals assigned incorrectly - -
    Dihedrals read in from the data file were not assigned correctly to -atoms. This means there is something invalid about the topology -definitions. - -
    Dihedrals defined but no dihedral types - -
    The data file header lists dihedrals but no dihedral types. - -
    Dimension command after simulation box is defined - -
    The dimension command cannot be used after a read_data, -read_restart, or create_box command. - -
    Dispersion PPPMDisp order has been reduced below minorder - -
    The default minimum order is 2. This can be reset by the -kspace_modify minorder command. - -
    Displace_atoms command before simulation box is defined - -
    The displace_atoms command cannot be used before a read_data, -read_restart, or create_box command. - -
    Distance must be > 0 for compute event/displace - -
    Self-explanatory. - -
    Divide by 0 in influence function - -
    This should not normally occur. It is likely a problem with your -model. - -
    Divide by 0 in influence function of pair peri/lps - -
    This should not normally occur. It is likely a problem with your -model. - -
    Divide by 0 in variable formula - -
    Self-explanatory. - -
    Domain too large for neighbor bins - -
    The domain has become extremely large so that neighbor bins cannot be -used. Most likely, one or more atoms have been blown out of the -simulation box to a great distance. - -
    Double precision is not supported on this accelerator - -
    Self-explanatory - -
    Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu - -
    Self-explanatory. - -
    Dump cfg arguments must start with 'mass type xs ys zs' or 'mass type xsu ysu zsu' - -
    This is a requirement of the CFG output format. See the dump cfg doc -page for more details. - -
    Dump cfg requires one snapshot per file - -
    Use the wildcard "*" character in the filename. - -
    Dump custom and fix not computed at compatible times - -
    The fix must produce per-atom quantities on timesteps that dump custom -needs them. - -
    Dump custom compute does not calculate per-atom array - -
    Self-explanatory. - -
    Dump custom compute does not calculate per-atom vector - -
    Self-explanatory. - -
    Dump custom compute does not compute per-atom info - -
    Self-explanatory. - -
    Dump custom compute vector is accessed out-of-range - -
    Self-explanatory. - -
    Dump custom fix does not compute per-atom array - -
    Self-explanatory. - -
    Dump custom fix does not compute per-atom info - -
    Self-explanatory. - -
    Dump custom fix does not compute per-atom vector - -
    Self-explanatory. - -
    Dump custom fix vector is accessed out-of-range - -
    Self-explanatory. - -
    Dump custom variable is not atom-style variable - -
    Only atom-style variables generate per-atom quantities, needed for -dump output. - -
    Dump dcd of non-matching # of atoms - -
    Every snapshot written by dump dcd must contain the same # of atoms. - -
    Dump dcd requires sorting by atom ID - -
    Use the dump_modify sort command to enable this. - -
    Dump every variable returned a bad timestep - -
    The variable must return a timestep greater than the current timestep. - -
    Dump file MPI-IO output not allowed with % in filename - -
    This is because a % signifies one file per processor and MPI-IO -creates one large file for all processors. - -
    Dump file does not contain requested snapshot - -
    Self-explanatory. - -
    Dump file is incorrectly formatted - -
    Self-explanatory. - -
    Dump image bond not allowed with no bond types - -
    Self-explanatory. - -
    Dump image cannot perform sorting - -
    Self-explanatory. - -
    Dump image persp option is not yet supported - -
    Self-explanatory. - -
    Dump image requires one snapshot per file - -
    Use a "*" in the filename. - -
    Dump local and fix not computed at compatible times - -
    The fix must produce per-atom quantities on timesteps that dump local -needs them. - -
    Dump local attributes contain no compute or fix - -
    Self-explanatory. - -
    Dump local cannot sort by atom ID - -
    This is because dump local does not really dump per-atom info. - -
    Dump local compute does not calculate local array - -
    Self-explanatory. - -
    Dump local compute does not calculate local vector - -
    Self-explanatory. - -
    Dump local compute does not compute local info - -
    Self-explanatory. - -
    Dump local compute vector is accessed out-of-range - -
    Self-explanatory. - -
    Dump local count is not consistent across input fields - -
    Every column of output must be the same length. - -
    Dump local fix does not compute local array - -
    Self-explanatory. - -
    Dump local fix does not compute local info - -
    Self-explanatory. - -
    Dump local fix does not compute local vector - -
    Self-explanatory. - -
    Dump local fix vector is accessed out-of-range - -
    Self-explanatory. - -
    Dump modify bcolor not allowed with no bond types - -
    Self-explanatory. - -
    Dump modify bdiam not allowed with no bond types - -
    Self-explanatory. - -
    Dump modify compute ID does not compute per-atom array - -
    Self-explanatory. - -
    Dump modify compute ID does not compute per-atom info - -
    Self-explanatory. - -
    Dump modify compute ID does not compute per-atom vector - -
    Self-explanatory. - -
    Dump modify compute ID vector is not large enough - -
    Self-explanatory. - -
    Dump modify element names do not match atom types - -
    Number of element names must equal number of atom types. - -
    Dump modify fix ID does not compute per-atom array - -
    Self-explanatory. - -
    Dump modify fix ID does not compute per-atom info - -
    Self-explanatory. - -
    Dump modify fix ID does not compute per-atom vector - -
    Self-explanatory. - -
    Dump modify fix ID vector is not large enough - -
    Self-explanatory. - -
    Dump modify variable is not atom-style variable - -
    Self-explanatory. - -
    Dump sort column is invalid - -
    Self-explanatory. - -
    Dump xtc requires sorting by atom ID - -
    Use the dump_modify sort command to enable this. - -
    Dump_modify buffer yes not allowed for this style - -
    Self-explanatory. - -
    Dump_modify format string is too short - -
    There are more fields to be dumped in a line of output than your -format string specifies. - -
    Dump_modify region ID does not exist - -
    Self-explanatory. - -
    Dumping an atom property that isn't allocated - -
    The chosen atom style does not define the per-atom quantity being -dumped. - -
    Duplicate fields in read_dump command - -
    Self-explanatory. - -
    Duplicate particle in PeriDynamic bond - simulation box is too small - -
    This is likely because your box length is shorter than 2 times -the bond length. - -
    Electronic temperature dropped below zero - -
    Something has gone wrong with the fix ttm electron temperature model. - -
    Empty brackets in variable - -
    There is no variable syntax that uses empty brackets. Check -the variable doc page. - -
    Energy was not tallied on needed timestep - -
    You are using a thermo keyword that requires potentials to -have tallied energy, but they didn't on this timestep. See the -variable doc page for ideas on how to make this work. - -
    Epsilon or sigma reference not set by pair style in PPPMDisp - -
    Self-explanatory. - -
    Epsilon or sigma reference not set by pair style in ewald/n - -
    The pair style is not providing the needed epsilon or sigma values. - -
    Error in vdw spline: inner radius > outer radius - -
    A pre-tabulated spline is invalid. Likely a problem with the -potential parameters. - -
    Failed to allocate %ld bytes for array %s - -
    Your LAMMPS simulation has run out of memory. You need to run a -smaller simulation or on more processors. - -
    Failed to open FFmpeg pipeline to file %s - -
    The specified file cannot be opened. Check that the path and name are -correct and writable and that the FFmpeg executable can be found and run. - -
    Failed to reallocate %ld bytes for array %s - -
    Your LAMMPS simulation has run out of memory. You need to run a -smaller simulation or on more processors. - -
    Fewer SRD bins than processors in some dimension - -
    This is not allowed. Make your SRD bin size smaller. - -
    File variable could not read value - -
    Check the file assigned to the variable. - -
    Final box dimension due to fix deform is < 0.0 - -
    Self-explanatory. - -
    Fix %s does not allow use of dynamic group - -
    Dynamic groups have not yet been enabled for this fix. - -
    Fix ID for compute chunk/atom does not exist - -
    Self-explanatory. - -
    Fix ID for compute erotate/rigid does not exist - -
    Self-explanatory. - -
    Fix ID for compute ke/rigid does not exist - -
    Self-explanatory. - -
    Fix ID for compute reduce does not exist - -
    Self-explanatory. - -
    Fix ID for compute slice does not exist - -
    Self-explanatory. - -
    Fix ID for fix ave/atom does not exist - -
    Self-explanatory. - -
    Fix ID for fix ave/chunk does not exist - -
    Self-explanatory. - -
    Fix ID for fix ave/correlate does not exist - -
    Self-explanatory. - -
    Fix ID for fix ave/histo does not exist - -
    Self-explanatory. - -
    Fix ID for fix ave/spatial does not exist - -
    Self-explanatory. - -
    Fix ID for fix ave/time does not exist - -
    Self-explanatory. - -
    Fix ID for fix store/state does not exist - -
    Self-explanatory - -
    Fix ID for fix vector does not exist - -
    Self-explanatory. - -
    Fix ID for read_data does not exist - -
    Self-explanatory. - -
    Fix ID for velocity does not exist - -
    Self-explanatory. - -
    Fix ID must be alphanumeric or underscore characters - -
    Self-explanatory. - -
    Fix SRD: bad bin assignment for SRD advection - -
    Something has gone wrong in your SRD model; try using more -conservative settings. - -
    Fix SRD: bad search bin assignment - -
    Something has gone wrong in your SRD model; try using more -conservative settings. - -
    Fix SRD: bad stencil bin for big particle - -
    Something has gone wrong in your SRD model; try using more -conservative settings. - -
    Fix SRD: too many big particles in bin - -
    Reset the ATOMPERBIN parameter at the top of fix_srd.cpp -to a larger value, and re-compile the code. - -
    Fix SRD: too many walls in bin - -
    This should not happen unless your system has been setup incorrectly. - -
    Fix adapt interface to this pair style not supported - -
    New coding for the pair style would need to be done. - -
    Fix adapt kspace style does not exist - -
    Self-explanatory. - -
    Fix adapt pair style does not exist - -
    Self-explanatory - -
    Fix adapt pair style param not supported - -
    The pair style does not know about the parameter you specified. - -
    Fix adapt requires atom attribute charge - -
    The atom style being used does not specify an atom charge. - -
    Fix adapt requires atom attribute diameter - -
    The atom style being used does not specify an atom diameter. - -
    Fix adapt type pair range is not valid for pair hybrid sub-style - -
    Self-explanatory. - -
    Fix append/atoms requires a lattice be defined - -
    Use the lattice command for this purpose. - -
    Fix ave/atom compute array is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/atom compute does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/atom compute does not calculate a per-atom vector - -
    A compute used by fix ave/atom must generate per-atom values. - -
    Fix ave/atom compute does not calculate per-atom values - -
    A compute used by fix ave/atom must generate per-atom values. - -
    Fix ave/atom fix array is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/atom fix does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/atom fix does not calculate a per-atom vector - -
    A fix used by fix ave/atom must generate per-atom values. - -
    Fix ave/atom fix does not calculate per-atom values - -
    A fix used by fix ave/atom must generate per-atom values. - -
    Fix ave/atom variable is not atom-style variable - -
    A variable used by fix ave/atom must generate per-atom values. - -
    Fix ave/chunk compute does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/chunk compute does not calculate a per-atom vector - -
    Self-explanatory. - -
    Fix ave/chunk compute does not calculate per-atom values - -
    Self-explanatory. - -
    Fix ave/chunk compute vector is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/chunk does not use chunk/atom compute - -
    The specified conpute is not for a compute chunk/atom command. - -
    Fix ave/chunk fix does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/chunk fix does not calculate a per-atom vector - -
    Self-explanatory. - -
    Fix ave/chunk fix does not calculate per-atom values - -
    Self-explanatory. - -
    Fix ave/chunk fix vector is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/chunk variable is not atom-style variable - -
    Self-explanatory. - -
    Fix ave/correlate compute does not calculate a scalar - -
    Self-explanatory. - -
    Fix ave/correlate compute does not calculate a vector - -
    Self-explanatory. - -
    Fix ave/correlate compute vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Fix ave/correlate fix does not calculate a scalar - -
    Self-explanatory. - -
    Fix ave/correlate fix does not calculate a vector - -
    Self-explanatory. - -
    Fix ave/correlate fix vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Fix ave/correlate variable is not equal-style variable - -
    Self-explanatory. - -
    Fix ave/histo cannot input local values in scalar mode - -
    Self-explanatory. - -
    Fix ave/histo cannot input per-atom values in scalar mode - -
    Self-explanatory. - -
    Fix ave/histo compute array is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate a global array - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate a global scalar - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate a global vector - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate a local array - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate a local vector - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate a per-atom vector - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate local values - -
    Self-explanatory. - -
    Fix ave/histo compute does not calculate per-atom values - -
    Self-explanatory. - -
    Fix ave/histo compute vector is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/histo fix array is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate a global array - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate a global scalar - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate a global vector - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate a local array - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate a local vector - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate a per-atom vector - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate local values - -
    Self-explanatory. - -
    Fix ave/histo fix does not calculate per-atom values - -
    Self-explanatory. - -
    Fix ave/histo fix vector is accessed out-of-range - -
    Self-explanatory. - -
    Fix ave/histo input is invalid compute - -
    Self-explanatory. - -
    Fix ave/histo input is invalid fix - -
    Self-explanatory. - -
    Fix ave/histo input is invalid variable - -
    Self-explanatory. - -
    Fix ave/histo inputs are not all global, peratom, or local - -
    All inputs in a single fix ave/histo command must be of the -same style. - -
    Fix ave/spatial compute does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/spatial compute does not calculate a per-atom vector - -
    A compute used by fix ave/spatial must generate per-atom values. - -
    Fix ave/spatial compute does not calculate per-atom values - -
    A compute used by fix ave/spatial must generate per-atom values. - -
    Fix ave/spatial compute vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Fix ave/spatial fix does not calculate a per-atom array - -
    Self-explanatory. - -
    Fix ave/spatial fix does not calculate a per-atom vector - -
    A fix used by fix ave/spatial must generate per-atom values. - -
    Fix ave/spatial fix does not calculate per-atom values - -
    A fix used by fix ave/spatial must generate per-atom values. - -
    Fix ave/spatial fix vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Fix ave/spatial for triclinic boxes requires units reduced - -
    Self-explanatory. - -
    Fix ave/spatial settings invalid with changing box size - -
    If the box size changes, only the units reduced option can be -used. - -
    Fix ave/spatial variable is not atom-style variable - -
    A variable used by fix ave/spatial must generate per-atom values. - -
    Fix ave/time cannot set output array intensive/extensive from these inputs - -
    One of more of the vector inputs has individual elements which are -flagged as intensive or extensive. Such an input cannot be flagged as -all intensive/extensive when turned into an array by fix ave/time. - -
    Fix ave/time cannot use variable with vector mode - -
    Variables produce scalar values. - -
    Fix ave/time columns are inconsistent lengths - -
    Self-explanatory. - -
    Fix ave/time compute array is accessed out-of-range - -
    An index for the array is out of bounds. - -
    Fix ave/time compute does not calculate a scalar - -
    Self-explantory. - -
    Fix ave/time compute does not calculate a vector - -
    Self-explantory. - -
    Fix ave/time compute does not calculate an array - -
    Self-explanatory. - -
    Fix ave/time compute vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Fix ave/time fix array cannot be variable length - -
    Self-explanatory. - -
    Fix ave/time fix array is accessed out-of-range - -
    An index for the array is out of bounds. - -
    Fix ave/time fix does not calculate a scalar - -
    Self-explanatory. - -
    Fix ave/time fix does not calculate a vector - -
    Self-explanatory. - -
    Fix ave/time fix does not calculate an array - -
    Self-explanatory. - -
    Fix ave/time fix vector cannot be variable length - -
    Self-explanatory. - -
    Fix ave/time fix vector is accessed out-of-range - -
    The index for the vector is out of bounds. - -
    Fix ave/time variable is not equal-style variable - -
    Self-explanatory. - -
    Fix balance rcb cannot be used with comm_style brick - -
    Comm_style tiled must be used instead. - -
    Fix balance shift string is invalid - -
    The string can only contain the characters "x", "y", or "z". - -
    Fix bond/break needs ghost atoms from further away - -
    This is because the fix needs to walk bonds to a certain distance to -acquire needed info, The comm_modify cutoff command can be used to -extend the communication range. - -
    Fix bond/create angle type is invalid - -
    Self-explanatory. - -
    Fix bond/create cutoff is longer than pairwise cutoff - -
    This is not allowed because bond creation is done using the -pairwise neighbor list. - -
    Fix bond/create dihedral type is invalid - -
    Self-explanatory. - -
    Fix bond/create improper type is invalid - -
    Self-explanatory. - -
    Fix bond/create induced too many angles/dihedrals/impropers per atom - -
    See the read_data command for info on setting the "extra angle per -atom", etc header values to allow for additional angles, etc to be -formed. - -
    Fix bond/create needs ghost atoms from further away - -
    This is because the fix needs to walk bonds to a certain distance to -acquire needed info, The comm_modify cutoff command can be used to -extend the communication range. - -
    Fix bond/swap cannot use dihedral or improper styles - -
    These styles cannot be defined when using this fix. - -
    Fix bond/swap requires pair and bond styles - -
    Self-explanatory. - -
    Fix bond/swap requires special_bonds = 0,1,1 - -
    Self-explanatory. - -
    Fix box/relax generated negative box length - -
    The pressure being applied is likely too large. Try applying -it incrementally, to build to the high pressure. - -
    Fix command before simulation box is defined - -
    The fix command cannot be used before a read_data, read_restart, or -create_box command. - -
    Fix deform cannot use yz variable with xy - -
    The yz setting cannot be a variable if xy deformation is also -specified. This is because LAMMPS cannot determine if the yz setting -will induce a box flip which would be invalid if xy is also changing. - -
    Fix deform is changing yz too much with xy - -
    When both yz and xy are changing, it induces changes in xz if the -box must flip from one tilt extreme to another. Thus it is not -allowed for yz to grow so much that a flip is induced. - -
    Fix deform tilt factors require triclinic box - -
    Cannot deform the tilt factors of a simulation box unless it -is a triclinic (non-orthogonal) box. - -
    Fix deform volume setting is invalid - -
    Cannot use volume style unless other dimensions are being controlled. - -
    Fix deposit and fix rigid/small not using same molecule template ID - -
    Self-explanatory. - -
    Fix deposit and fix shake not using same molecule template ID - -
    Self-explanatory. - -
    Fix deposit molecule must have atom types - -
    The defined molecule does not specify atom types. - -
    Fix deposit molecule must have coordinates - -
    The defined molecule does not specify coordinates. - -
    Fix deposit molecule template ID must be same as atom_style template ID - -
    When using atom_style template, you cannot deposit molecules that are -not in that template. - -
    Fix deposit region cannot be dynamic - -
    Only static regions can be used with fix deposit. - -
    Fix deposit region does not support a bounding box - -
    Not all regions represent bounded volumes. You cannot use -such a region with the fix deposit command. - -
    Fix deposit shake fix does not exist - -
    Self-explanatory. - -
    Fix efield requires atom attribute q or mu - -
    The atom style defined does not have this attribute. - -
    Fix efield with dipoles cannot use atom-style variables - -
    This option is not supported. - -
    Fix evaporate molecule requires atom attribute molecule - -
    The atom style being used does not define a molecule ID. - -
    Fix external callback function not set - -
    This must be done by an external program in order to use this fix. - -
    Fix for fix ave/atom not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix ave/atom is -requesting a value on a non-allowed timestep. - -
    Fix for fix ave/chunk not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix ave/chunk is -requesting a value on a non-allowed timestep. - -
    Fix for fix ave/correlate not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix ave/correlate -is requesting a value on a non-allowed timestep. - -
    Fix for fix ave/histo not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix ave/histo is -requesting a value on a non-allowed timestep. - -
    Fix for fix ave/spatial not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix ave/spatial is -requesting a value on a non-allowed timestep. - -
    Fix for fix ave/time not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix ave/time -is requesting a value on a non-allowed timestep. - -
    Fix for fix store/state not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix store/state -is requesting a value on a non-allowed timestep. - -
    Fix for fix vector not computed at compatible time - -
    Fixes generate their values on specific timesteps. Fix vector is -requesting a value on a non-allowed timestep. - -
    Fix freeze requires atom attribute torque - -
    The atom style defined does not have this attribute. - -
    Fix gcmc and fix shake not using same molecule template ID - -
    Self-explanatory. - -
    Fix gcmc cannot exchange individual atoms belonging to a molecule - -
    This is an error since you should not delete only one atom of a -molecule. The user has specified atomic (non-molecular) gas -exchanges, but an atom belonging to a molecule could be deleted. - -
    Fix gcmc does not (yet) work with atom_style template - -
    Self-explanatory. - -
    Fix gcmc molecule command requires that atoms have molecule attributes - -
    Should not choose the gcmc molecule feature if no molecules are being -simulated. The general molecule flag is off, but gcmc's molecule flag -is on. - -
    Fix gcmc molecule must have atom types - -
    The defined molecule does not specify atom types. - -
    Fix gcmc molecule must have coordinates - -
    The defined molecule does not specify coordinates. - -
    Fix gcmc molecule template ID must be same as atom_style template ID - -
    When using atom_style template, you cannot insert molecules that are -not in that template. - -
    Fix gcmc ran out of available atom IDs - -
    See the setting for tagint in the src/lmptype.h file. - -
    Fix gcmc ran out of available molecule IDs - -
    See the setting for tagint in the src/lmptype.h file. - -
    Fix gcmc region cannot be dynamic - -
    Only static regions can be used with fix gcmc. - -
    Fix gcmc region does not support a bounding box - -
    Not all regions represent bounded volumes. You cannot use -such a region with the fix gcmc command. - -
    Fix gcmc region extends outside simulation box - -
    Self-explanatory. - -
    Fix gcmc shake fix does not exist - -
    Self-explanatory. - -
    Fix gld c coefficients must be >= 0 - -
    Self-explanatory. - -
    Fix gld needs more prony series coefficients - -
    Self-explanatory. - -
    Fix gld prony terms must be > 0 - -
    Self-explanatory. - -
    Fix gld series type must be pprony for now - -
    Self-explanatory. - -
    Fix gld start temperature must be >= 0 - -
    Self-explanatory. - -
    Fix gld stop temperature must be >= 0 - -
    Self-explanatory. - -
    Fix gld tau coefficients must be > 0 - -
    Self-explanatory. - -
    Fix heat group has no atoms - -
    Self-explanatory. - -
    Fix heat kinetic energy of an atom went negative - -
    This will cause the velocity rescaling about to be performed by fix -heat to be invalid. - -
    Fix heat kinetic energy went negative - -
    This will cause the velocity rescaling about to be performed by fix -heat to be invalid. - -
    Fix in variable not computed at compatible time - -
    Fixes generate their values on specific timesteps. The variable is -requesting the values on a non-allowed timestep. - -
    Fix langevin angmom is not yet implemented with kokkos - -
    This option is not yet available. - -
    Fix langevin angmom requires atom style ellipsoid - -
    Self-explanatory. - -
    Fix langevin angmom requires extended particles - -
    This fix option cannot be used with point paritlces. - -
    Fix langevin omega is not yet implemented with kokkos - -
    This option is not yet available. - -
    Fix langevin omega requires atom style sphere - -
    Self-explanatory. - -
    Fix langevin omega requires extended particles - -
    One of the particles has radius 0.0. - -
    Fix langevin period must be > 0.0 - -
    The time window for temperature relaxation must be > 0 - -
    Fix langevin variable returned negative temperature - -
    Self-explanatory. - -
    Fix momentum group has no atoms - -
    Self-explanatory. - -
    Fix move cannot define z or vz variable for 2d problem - -
    Self-explanatory. - -
    Fix move cannot rotate aroung non z-axis for 2d problem - -
    Self-explanatory. - -
    Fix move cannot set linear z motion for 2d problem - -
    Self-explanatory. - -
    Fix move cannot set wiggle z motion for 2d problem - -
    Self-explanatory. - -
    Fix msst compute ID does not compute potential energy - -
    Self-explanatory. - -
    Fix msst compute ID does not compute pressure - -
    Self-explanatory. - -
    Fix msst compute ID does not compute temperature - -
    Self-explanatory. - -
    Fix msst requires a periodic box - -
    Self-explanatory. - -
    Fix msst tscale must satisfy 0 <= tscale < 1 - -
    Self-explanatory. - -
    Fix npt/nph has tilted box too far in one step - periodic cell is too far from equilibrium state - -
    Self-explanatory. The change in the box tilt is too extreme -on a short timescale. - -
    Fix nve/asphere requires extended particles - -
    This fix can only be used for particles with a shape setting. - -
    Fix nve/asphere/noforce requires atom style ellipsoid - -
    Self-explanatory. - -
    Fix nve/asphere/noforce requires extended particles - -
    One of the particles is not an ellipsoid. - -
    Fix nve/body requires atom style body - -
    Self-explanatory. - -
    Fix nve/body requires bodies - -
    This fix can only be used for particles that are bodies. - -
    Fix nve/line can only be used for 2d simulations - -
    Self-explanatory. - -
    Fix nve/line requires atom style line - -
    Self-explanatory. - -
    Fix nve/line requires line particles - -
    Self-explanatory. - -
    Fix nve/sphere requires atom attribute mu - -
    An atom style with this attribute is needed. - -
    Fix nve/sphere requires atom style sphere - -
    Self-explanatory. - -
    Fix nve/sphere requires extended particles - -
    This fix can only be used for particles of a finite size. - -
    Fix nve/tri can only be used for 3d simulations - -
    Self-explanatory. - -
    Fix nve/tri requires atom style tri - -
    Self-explanatory. - -
    Fix nve/tri requires tri particles - -
    Self-explanatory. - -
    Fix nvt/nph/npt asphere requires extended particles - -
    The shape setting for a particle in the fix group has shape = 0.0, -which means it is a point particle. - -
    Fix nvt/nph/npt sphere requires atom style sphere - -
    Self-explanatory. - -
    Fix nvt/npt/nph damping parameters must be > 0.0 - -
    Self-explanatory. - -
    Fix nvt/npt/nph dilate group ID does not exist - -
    Self-explanatory. - -
    Fix nvt/sphere requires extended particles - -
    This fix can only be used for particles of a finite size. - -
    Fix orient/fcc file open failed - -
    The fix orient/fcc command could not open a specified file. - -
    Fix orient/fcc file read failed - -
    The fix orient/fcc command could not read the needed parameters from a -specified file. - -
    Fix orient/fcc found self twice - -
    The neighbor lists used by fix orient/fcc are messed up. If this -error occurs, it is likely a bug, so send an email to the -developers. - -
    Fix peri neigh does not exist - -
    Somehow a fix that the pair style defines has been deleted. - -
    Fix pour and fix rigid/small not using same molecule template ID - -
    Self-explanatory. - -
    Fix pour and fix shake not using same molecule template ID - -
    Self-explanatory. - -
    Fix pour insertion count per timestep is 0 - -
    Self-explanatory. - -
    Fix pour molecule must have atom types - -
    The defined molecule does not specify atom types. - -
    Fix pour molecule must have coordinates - -
    The defined molecule does not specify coordinates. - -
    Fix pour molecule template ID must be same as atom style template ID - -
    When using atom_style template, you cannot pour molecules that are -not in that template. - -
    Fix pour polydisperse fractions do not sum to 1.0 - -
    Self-explanatory. - -
    Fix pour region ID does not exist - -
    Self-explanatory. - -
    Fix pour region cannot be dynamic - -
    Only static regions can be used with fix pour. - -
    Fix pour region does not support a bounding box - -
    Not all regions represent bounded volumes. You cannot use -such a region with the fix pour command. - -
    Fix pour requires atom attributes radius, rmass - -
    The atom style defined does not have these attributes. - -
    Fix pour rigid fix does not exist - -
    Self-explanatory. - -
    Fix pour shake fix does not exist - -
    Self-explanatory. - -
    Fix press/berendsen damping parameters must be > 0.0 - -
    Self-explanatory. - -
    Fix property/atom cannot specify mol twice - -
    Self-explanatory. - -
    Fix property/atom cannot specify q twice - -
    Self-explanatory. - -
    Fix property/atom mol when atom_style already has molecule attribute - -
    Self-explanatory. - -
    Fix property/atom q when atom_style already has charge attribute - -
    Self-explanatory. - -
    Fix property/atom vector name already exists - -
    The name for an integer or floating-point vector must be unique. - -
    Fix qeq has negative upper Taper radius cutoff - -
    Self-explanatory. - -
    Fix qeq/comb group has no atoms - -
    Self-explanatory. - -
    Fix qeq/comb requires atom attribute q - -
    An atom style with charge must be used to perform charge equilibration. - -
    Fix qeq/dynamic group has no atoms - -
    Self-explanatory. - -
    Fix qeq/dynamic requires atom attribute q - -
    Self-explanatory. - -
    Fix qeq/point group has no atoms - -
    Self-explanatory. - -
    Fix qeq/point has insufficient QEq matrix size - -
    Occurs when number of neighbor atoms for an atom increased too much -during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. - -
    Fix qeq/point requires atom attribute q - -
    Self-explanatory. - -
    Fix qeq/shielded group has no atoms - -
    Self-explanatory. - -
    Fix qeq/shielded has insufficient QEq matrix size - -
    Occurs when number of neighbor atoms for an atom increased too much -during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. - -
    Fix qeq/shielded requires atom attribute q - -
    Self-explanatory. - -
    Fix qeq/slater could not extract params from pair coul/streitz - -
    This should not happen unless pair coul/streitz has been altered. - -
    Fix qeq/slater group has no atoms - -
    Self-explanatory. - -
    Fix qeq/slater has insufficient QEq matrix size - -
    Occurs when number of neighbor atoms for an atom increased too much -during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. - -
    Fix qeq/slater requires atom attribute q - -
    Self-explanatory. - -
    Fix reax/bonds numbonds > nsbmax_most - -
    The limit of the number of bonds expected by the ReaxFF force field -was exceeded. - -
    Fix recenter group has no atoms - -
    Self-explanatory. - -
    Fix restrain requires an atom map, see atom_modify - -
    Self-explanatory. - -
    Fix rigid atom has non-zero image flag in a non-periodic dimension - -
    Image flags for non-periodic dimensions should not be set. - -
    Fix rigid file has no lines - -
    Self-explanatory. - -
    Fix rigid langevin period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid molecule requires atom attribute molecule - -
    Self-explanatory. - -
    Fix rigid npt/nph dilate group ID does not exist - -
    Self-explanatory. - -
    Fix rigid npt/nph does not yet allow triclinic box - -
    This is a current restriction in LAMMPS. - -
    Fix rigid npt/nph period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid npt/small t_chain should not be less than 1 - -
    Self-explanatory. - -
    Fix rigid npt/small t_order must be 3 or 5 - -
    Self-explanatory. - -
    Fix rigid nvt/npt/nph damping parameters must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid nvt/small t_chain should not be less than 1 - -
    Self-explanatory. - -
    Fix rigid nvt/small t_iter should not be less than 1 - -
    Self-explanatory. - -
    Fix rigid nvt/small t_order must be 3 or 5 - -
    Self-explanatory. - -
    Fix rigid xy torque cannot be on for 2d simulation - -
    Self-explanatory. - -
    Fix rigid z force cannot be on for 2d simulation - -
    Self-explanatory. - -
    Fix rigid/npt period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid/npt temperature order must be 3 or 5 - -
    Self-explanatory. - -
    Fix rigid/npt/small period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid/nvt period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid/nvt temperature order must be 3 or 5 - -
    Self-explanatory. - -
    Fix rigid/nvt/small period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid/small atom has non-zero image flag in a non-periodic dimension - -
    Image flags for non-periodic dimensions should not be set. - -
    Fix rigid/small langevin period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid/small molecule must have atom types - -
    The defined molecule does not specify atom types. - -
    Fix rigid/small molecule must have coordinates - -
    The defined molecule does not specify coordinates. - -
    Fix rigid/small npt/nph period must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid/small nvt/npt/nph damping parameters must be > 0.0 - -
    Self-explanatory. - -
    Fix rigid/small nvt/npt/nph dilate group ID does not exist - -
    Self-explanatory. - -
    Fix rigid/small requires an atom map, see atom_modify - -
    Self-explanatory. - -
    Fix rigid/small requires atom attribute molecule - -
    Self-explanatory. - -
    Fix rigid: Bad principal moments - -
    The principal moments of inertia computed for a rigid body -are not within the required tolerances. - -
    Fix shake cannot be used with minimization - -
    Cannot use fix shake while doing an energy minimization since -it turns off bonds that should contribute to the energy. - -
    Fix shake molecule template must have shake info - -
    The defined molecule does not specify SHAKE information. - -
    Fix spring couple group ID does not exist - -
    Self-explanatory. - -
    Fix srd can only currently be used with comm_style brick - -
    This is a current restriction in LAMMPS. - -
    Fix srd lamda must be >= 0.6 of SRD grid size - -
    This is a requirement for accuracy reasons. - -
    Fix srd no-slip requires atom attribute torque - -
    This is because the SRD collisions will impart torque to the solute -particles. - -
    Fix srd requires SRD particles all have same mass - -
    Self-explanatory. - -
    Fix srd requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Fix srd requires newton pair on - -
    Self-explanatory. - -
    Fix store/state compute array is accessed out-of-range - -
    Self-explanatory. - -
    Fix store/state compute does not calculate a per-atom array - -
    The compute calculates a per-atom vector. - -
    Fix store/state compute does not calculate a per-atom vector - -
    The compute calculates a per-atom vector. - -
    Fix store/state compute does not calculate per-atom values - -
    Computes that calculate global or local quantities cannot be used -with fix store/state. - -
    Fix store/state fix array is accessed out-of-range - -
    Self-explanatory. - -
    Fix store/state fix does not calculate a per-atom array - -
    The fix calculates a per-atom vector. - -
    Fix store/state fix does not calculate a per-atom vector - -
    The fix calculates a per-atom array. - -
    Fix store/state fix does not calculate per-atom values - -
    Fixes that calculate global or local quantities cannot be used with -fix store/state. - -
    Fix store/state for atom property that isn't allocated - -
    Self-explanatory. - -
    Fix store/state variable is not atom-style variable - -
    Only atom-style variables calculate per-atom quantities. - -
    Fix temp/berendsen period must be > 0.0 - -
    Self-explanatory. - -
    Fix temp/berendsen variable returned negative temperature - -
    Self-explanatory. - -
    Fix temp/csvr is not compatible with fix shake - -
    These two commands cannot currently be used toghether. - -
    Fix temp/csvr variable returned negative temperature - -
    Self-explanatory. - -
    Fix temp/rescale variable returned negative temperature - -
    Self-explanatory. - -
    Fix tfmc displacement length must be > 0 - -
    Self-explanatory. - -
    Fix tfmc is not compatible with fix shake - -
    These two commands cannot currently be used together. - -
    Fix tfmc temperature must be > 0 - -
    Self-explanatory. - -
    Fix thermal/conductivity swap value must be positive - -
    Self-explanatory. - -
    Fix tmd must come after integration fixes - -
    Any fix tmd command must appear in the input script after all time -integration fixes (nve, nvt, npt). See the fix tmd documentation for -details. - -
    Fix ttm electron temperatures must be > 0.0 - -
    Self-explanatory. - -
    Fix ttm electronic_density must be > 0.0 - -
    Self-explanatory. - -
    Fix ttm electronic_specific_heat must be > 0.0 - -
    Self-explanatory. - -
    Fix ttm electronic_thermal_conductivity must be >= 0.0 - -
    Self-explanatory. - -
    Fix ttm gamma_p must be > 0.0 - -
    Self-explanatory. - -
    Fix ttm gamma_s must be >= 0.0 - -
    Self-explanatory. - -
    Fix ttm number of nodes must be > 0 - -
    Self-explanatory. - -
    Fix ttm v_0 must be >= 0.0 - -
    Self-explanatory. - -
    Fix used in compute chunk/atom not computed at compatible time - -
    The chunk/atom compute cannot query the output of the fix on a timestep -it is needed. - -
    Fix used in compute reduce not computed at compatible time - -
    Fixes generate their values on specific timesteps. Compute reduce is -requesting a value on a non-allowed timestep. - -
    Fix used in compute slice not computed at compatible time - -
    Fixes generate their values on specific timesteps. Compute slice is -requesting a value on a non-allowed timestep. - -
    Fix vector cannot set output array intensive/extensive from these inputs - -
    The inputs to the command have conflicting intensive/extensive attributes. -You need to use more than one fix vector command. - -
    Fix vector compute does not calculate a scalar - -
    Self-explanatory. - -
    Fix vector compute does not calculate a vector - -
    Self-explanatory. - -
    Fix vector compute vector is accessed out-of-range - -
    Self-explanatory. - -
    Fix vector fix does not calculate a scalar - -
    Self-explanatory. - -
    Fix vector fix does not calculate a vector - -
    Self-explanatory. - -
    Fix vector fix vector is accessed out-of-range - -
    Self-explanatory. - -
    Fix vector variable is not equal-style variable - -
    Self-explanatory. - -
    Fix viscosity swap value must be positive - -
    Self-explanatory. - -
    Fix viscosity vtarget value must be positive - -
    Self-explanatory. - -
    Fix wall cutoff <= 0.0 - -
    Self-explanatory. - -
    Fix wall/colloid requires atom style sphere - -
    Self-explanatory. - -
    Fix wall/colloid requires extended particles - -
    One of the particles has radius 0.0. - -
    Fix wall/gran is incompatible with Pair style - -
    Must use a granular pair style to define the parameters needed for -this fix. - -
    Fix wall/gran requires atom style sphere - -
    Self-explanatory. - -
    Fix wall/piston command only available at zlo - -
    The face keyword must be zlo. - -
    Fix wall/region colloid requires atom style sphere - -
    Self-explanatory. - -
    Fix wall/region colloid requires extended particles - -
    One of the particles has radius 0.0. - -
    Fix wall/region cutoff <= 0.0 - -
    Self-explanatory. - -
    Fix_modify pressure ID does not compute pressure - -
    The compute ID assigned to the fix must compute pressure. - -
    Fix_modify temperature ID does not compute temperature - -
    The compute ID assigned to the fix must compute temperature. - -
    For triclinic deformation, specified target stress must be hydrostatic - -
    Triclinic pressure control is allowed using the tri keyword, but -non-hydrostatic pressure control can not be used in this case. - -
    Found no restart file matching pattern - -
    When using a "*" in the restart file name, no matching file was found. - -
    GPU library not compiled for this accelerator - -
    Self-explanatory. - -
    GPU package does not (yet) work with atom_style template - -
    Self-explanatory. - -
    GPU particle split must be set to 1 for this pair style. - -
    For this pair style, you cannot run part of the force calculation on -the host. See the package command. - -
    GPU split param must be positive for hybrid pair styles - -
    See the package gpu command. - -
    Ghost velocity forward comm not yet implemented with Kokkos - -
    This is a current restriction. - -
    Gmask function in equal-style variable formula - -
    Gmask is per-atom operation. - -
    Gravity changed since fix pour was created - -
    The gravity vector defined by fix gravity must be static. - -
    Gravity must point in -y to use with fix pour in 2d - -
    Self-explanatory. - -
    Gravity must point in -z to use with fix pour in 3d - -
    Self-explanatory. - -
    Grmask function in equal-style variable formula - -
    Grmask is per-atom operation. - -
    Group ID does not exist - -
    A group ID used in the group command does not exist. - -
    Group ID in variable formula does not exist - -
    Self-explanatory. - -
    Group all cannot be made dynamic - -
    This operation is not allowed. - -
    Group command before simulation box is defined - -
    The group command cannot be used before a read_data, read_restart, or -create_box command. - -
    Group dynamic cannot reference itself - -
    Self-explanatory. - -
    Group dynamic parent group cannot be dynamic - -
    Self-explanatory. - -
    Group dynamic parent group does not exist - -
    Self-explanatory. - -
    Group region ID does not exist - -
    A region ID used in the group command does not exist. - -
    If read_dump purges it cannot replace or trim - -
    These operations are not compatible. See the read_dump doc -page for details. - -
    Illegal ... command - -
    Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -
    Illegal COMB parameter - -
    One or more of the coefficients defined in the potential file is -invalid. - -
    Illegal COMB3 parameter - -
    One or more of the coefficients defined in the potential file is -invalid. - -
    Illegal Stillinger-Weber parameter - -
    One or more of the coefficients defined in the potential file is -invalid. - -
    Illegal Tersoff parameter - -
    One or more of the coefficients defined in the potential file is -invalid. - -
    Illegal compute voronoi/atom command (occupation and (surface or edges)) - -
    Self-explanatory. - -
    Illegal coul/streitz parameter - -
    One or more of the coefficients defined in the potential file is -invalid. - -
    Illegal dump_modify sfactor value (must be > 0.0) - -
    Self-explanatory. - -
    Illegal dump_modify tfactor value (must be > 0.0) - -
    Self-explanatory. - -
    Illegal fix gcmc gas mass <= 0 - -
    The computed mass of the designated gas molecule or atom type was less -than or equal to zero. - -
    Illegal fix tfmc random seed - -
    Seeds can only be nonzero positive integers. - -
    Illegal fix wall/piston velocity - -
    The piston velocity must be positive. - -
    Illegal integrate style - -
    Self-explanatory. - -
    Illegal nb3b/harmonic parameter - -
    One or more of the coefficients defined in the potential file is -invalid. - -
    Illegal number of angle table entries - -
    There must be at least 2 table entries. - -
    Illegal number of bond table entries - -
    There must be at least 2 table entries. - -
    Illegal number of pair table entries - -
    There must be at least 2 table entries. - -
    Illegal simulation box - -
    The lower bound of the simulation box is greater than the upper bound. - -
    Imageint setting in lmptype.h is invalid - -
    Imageint must be as large or larger than smallint. - -
    Imageint setting in lmptype.h is not compatible - -
    Format of imageint stored in restart file is not consistent with -LAMMPS version you are running. See the settings in src/lmptype.h - -
    Improper atom missing in delete_bonds - -
    The delete_bonds command cannot find one or more atoms in a particular -improper on a particular processor. The pairwise cutoff is too short -or the atoms are too far apart to make a valid improper. - -
    Improper atom missing in set command - -
    The set command cannot find one or more atoms in a particular improper -on a particular processor. The pairwise cutoff is too short or the -atoms are too far apart to make a valid improper. - -
    Improper atoms %d %d %d %d missing on proc %d at step %ld - -
    One or more of 4 atoms needed to compute a particular improper are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the improper has blown apart and an atom is -too far away. - -
    Improper atoms missing on proc %d at step %ld - -
    One or more of 4 atoms needed to compute a particular improper are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the improper has blown apart and an atom is -too far away. - -
    Improper coeff for hybrid has invalid style - -
    Improper style hybrid uses another improper style as one of its -coefficients. The improper style used in the improper_coeff command -or read from a restart file is not recognized. - -
    Improper coeffs are not set - -
    No improper coefficients have been assigned in the data file or via -the improper_coeff command. - -
    Improper style hybrid cannot have hybrid as an argument - -
    Self-explanatory. - -
    Improper style hybrid cannot have none as an argument - -
    Self-explanatory. - -
    Improper style hybrid cannot use same improper style twice - -
    Self-explanatory. - -
    Improper_coeff command before improper_style is defined - -
    Coefficients cannot be set in the data file or via the improper_coeff -command until an improper_style has been assigned. - -
    Improper_coeff command before simulation box is defined - -
    The improper_coeff command cannot be used before a read_data, -read_restart, or create_box command. - -
    Improper_coeff command when no impropers allowed - -
    The chosen atom style does not allow for impropers to be defined. - -
    Improper_style command when no impropers allowed - -
    The chosen atom style does not allow for impropers to be defined. - -
    Impropers assigned incorrectly - -
    Impropers read in from the data file were not assigned correctly to -atoms. This means there is something invalid about the topology -definitions. - -
    Impropers defined but no improper types - -
    The data file header lists improper but no improper types. - -
    Incomplete use of variables in create_atoms command - -
    The var and set options must be used together. - -
    Inconsistent iparam/jparam values in fix bond/create command - -
    If itype and jtype are the same, then their maxbond and newtype -settings must also be the same. - -
    Inconsistent line segment in data file - -
    The end points of the line segment are not equal distances from the -center point which is the atom coordinate. - -
    Inconsistent triangle in data file - -
    The centroid of the triangle as defined by the corner points is not -the atom coordinate. - -
    Inconsistent use of finite-size particles by molecule template molecules - -
    Not all of the molecules define a radius for their constituent -particles. - -
    Incorrect # of floating-point values in Bodies section of data file - -
    See doc page for body style. - -
    Incorrect # of integer values in Bodies section of data file - -
    See doc page for body style. - -
    Incorrect %s format in data file - -
    A section of the data file being read by fix property/atom does -not have the correct number of values per line. - -
    Incorrect SNAP parameter file - -
    The file cannot be parsed correctly, check its internal syntax. - -
    Incorrect args for angle coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Incorrect args for bond coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Incorrect args for dihedral coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Incorrect args for improper coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Incorrect args for pair coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Incorrect args in pair_style command - -
    Self-explanatory. - -
    Incorrect atom format in data file - -
    Number of values per atom line in the data file is not consistent with -the atom style. - -
    Incorrect atom format in neb file - -
    The number of fields per line is not what expected. - -
    Incorrect bonus data format in data file - -
    See the read_data doc page for a description of how various kinds of -bonus data must be formatted for certain atom styles. - -
    Incorrect boundaries with slab Ewald - -
    Must have periodic x,y dimensions and non-periodic z dimension to use -2d slab option with Ewald. - -
    Incorrect boundaries with slab EwaldDisp - -
    Must have periodic x,y dimensions and non-periodic z dimension to use -2d slab option with Ewald. - -
    Incorrect boundaries with slab PPPM - -
    Must have periodic x,y dimensions and non-periodic z dimension to use -2d slab option with PPPM. - -
    Incorrect boundaries with slab PPPMDisp - -
    Must have periodic x,y dimensions and non-periodic z dimension to use -2d slab option with pppm/disp. - -
    Incorrect element names in ADP potential file - -
    The element names in the ADP file do not match those requested. - -
    Incorrect element names in EAM potential file - -
    The element names in the EAM file do not match those requested. - -
    Incorrect format in COMB potential file - -
    Incorrect number of words per line in the potential file. - -
    Incorrect format in COMB3 potential file - -
    Incorrect number of words per line in the potential file. - -
    Incorrect format in MEAM potential file - -
    Incorrect number of words per line in the potential file. - -
    Incorrect format in SNAP coefficient file - -
    Incorrect number of words per line in the coefficient file. - -
    Incorrect format in SNAP parameter file - -
    Incorrect number of words per line in the parameter file. - -
    Incorrect format in Stillinger-Weber potential file - -
    Incorrect number of words per line in the potential file. - -
    Incorrect format in TMD target file - -
    Format of file read by fix tmd command is incorrect. - -
    Incorrect format in Tersoff potential file - -
    Incorrect number of words per line in the potential file. - -
    Incorrect format in coul/streitz potential file - -
    Incorrect number of words per line in the potential file. - -
    Incorrect format in nb3b/harmonic potential file - -
    Incorrect number of words per line in the potential file. - -
    Incorrect integer value in Bodies section of data file - -
    See doc page for body style. - -
    Incorrect multiplicity arg for dihedral coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Incorrect rigid body format in fix rigid file - -
    The number of fields per line is not what expected. - -
    Incorrect rigid body format in fix rigid/small file - -
    The number of fields per line is not what expected. - -
    Incorrect sign arg for dihedral coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Incorrect velocity format in data file - -
    Each atom style defines a format for the Velocity section -of the data file. The read-in lines do not match. - -
    Incorrect weight arg for dihedral coefficients - -
    Self-explanatory. Check the input script or data file. - -
    Index between variable brackets must be positive - -
    Self-explanatory. - -
    Indexed per-atom vector in variable formula without atom map - -
    Accessing a value from an atom vector requires the ability to lookup -an atom index, which is provided by an atom map. An atom map does not -exist (by default) for non-molecular problems. Using the atom_modify -map command will force an atom map to be created. - -
    Initial temperatures not all set in fix ttm - -
    Self-explantory. - -
    Input line quote not followed by whitespace - -
    An end quote must be followed by whitespace. - -
    Insertion region extends outside simulation box - -
    Self-explanatory. - -
    Insufficient Jacobi rotations for POEMS body - -
    Eigensolve for rigid body was not sufficiently accurate. - -
    Insufficient Jacobi rotations for body nparticle - -
    Eigensolve for rigid body was not sufficiently accurate. - -
    Insufficient Jacobi rotations for rigid body - -
    Eigensolve for rigid body was not sufficiently accurate. - -
    Insufficient Jacobi rotations for rigid molecule - -
    Eigensolve for rigid body was not sufficiently accurate. - -
    Insufficient Jacobi rotations for triangle - -
    The calculation of the intertia tensor of the triangle failed. This -should not happen if it is a reasonably shaped triangle. - -
    Insufficient memory on accelerator - -
    There is insufficient memory on one of the devices specified for the gpu -package - -
    Internal error in atom_style body - -
    This error should not occur. Contact the developers. - -
    Invalid -reorder N value - -
    Self-explanatory. - -
    Invalid Boolean syntax in if command - -
    Self-explanatory. - -
    Invalid Kokkos command-line args - -
    Self-explanatory. See Section 2.7 of the manual for details. - -
    Invalid LAMMPS restart file - -
    The file does not appear to be a LAMMPS restart file since -it doesn't contain the correct magic string at the beginning. - -
    Invalid REAX atom type - -
    There is a mis-match between LAMMPS atom types and the elements -listed in the ReaxFF force field file. - -
    Invalid angle table length - -
    Length must be 2 or greater. - -
    Invalid angle type in Angles section of data file - -
    Angle type must be positive integer and within range of specified angle -types. - -
    Invalid angle type in Angles section of molecule file - -
    Self-explanatory. - -
    Invalid angle type index for fix shake - -
    Self-explanatory. - -
    Invalid args for non-hybrid pair coefficients - -
    "NULL" is only supported in pair_coeff calls when using pair hybrid - -
    Invalid argument to factorial %d - -
    N must be >= 0 and <= 167, otherwise the factorial result is too -large. - -
    Invalid atom ID in %s section of data file - -
    An atom in a section of the data file being read by fix property/atom -has an invalid atom ID that is <= 0 or > the maximum existing atom ID. - -
    Invalid atom ID in Angles section of data file - -
    Atom IDs must be positive integers and within range of defined -atoms. - -
    Invalid atom ID in Angles section of molecule file - -
    Self-explanatory. - -
    Invalid atom ID in Atoms section of data file - -
    Atom IDs must be positive integers. - -
    Invalid atom ID in Bodies section of data file - -
    Atom IDs must be positive integers and within range of defined -atoms. - -
    Invalid atom ID in Bonds section of data file - -
    Atom IDs must be positive integers and within range of defined -atoms. - -
    Invalid atom ID in Bonds section of molecule file - -
    Self-explanatory. - -
    Invalid atom ID in Bonus section of data file - -
    Atom IDs must be positive integers and within range of defined -atoms. - -
    Invalid atom ID in Dihedrals section of data file - -
    Atom IDs must be positive integers and within range of defined -atoms. - -
    Invalid atom ID in Impropers section of data file - -
    Atom IDs must be positive integers and within range of defined -atoms. - -
    Invalid atom ID in Velocities section of data file - -
    Atom IDs must be positive integers and within range of defined -atoms. - -
    Invalid atom ID in dihedrals section of molecule file - -
    Self-explanatory. - -
    Invalid atom ID in impropers section of molecule file - -
    Self-explanatory. - -
    Invalid atom ID in variable file - -
    Self-explanatory. - -
    Invalid atom IDs in neb file - -
    An ID in the file was not found in the system. - -
    Invalid atom diameter in molecule file - -
    Diameters must be >= 0.0. - -
    Invalid atom mass for fix shake - -
    Mass specified in fix shake command must be > 0.0. - -
    Invalid atom mass in molecule file - -
    Masses must be > 0.0. - -
    Invalid atom type in Atoms section of data file - -
    Atom types must range from 1 to specified # of types. - -
    Invalid atom type in create_atoms command - -
    The create_box command specified the range of valid atom types. -An invalid type is being requested. - -
    Invalid atom type in create_atoms mol command - -
    The atom types in the defined molecule are added to the value -specified in the create_atoms command, as an offset. The final value -for each atom must be between 1 to N, where N is the number of atom -types. - -
    Invalid atom type in fix atom/swap command - -
    The atom type specified in the atom/swap command does not exist. - -
    Invalid atom type in fix bond/create command - -
    Self-explanatory. - -
    Invalid atom type in fix deposit command - -
    Self-explanatory. - -
    Invalid atom type in fix deposit mol command - -
    The atom types in the defined molecule are added to the value -specified in the create_atoms command, as an offset. The final value -for each atom must be between 1 to N, where N is the number of atom -types. - -
    Invalid atom type in fix gcmc command - -
    The atom type specified in the gcmc command does not exist. - -
    Invalid atom type in fix gcmc mol command - -
    Self-explanatory. - -
    Invalid atom type in fix pour command - -
    Self-explanatory. - -
    Invalid atom type in fix pour mol command - -
    The atom types in the defined molecule are added to the value -specified in the create_atoms command, as an offset. The final value -for each atom must be between 1 to N, where N is the number of atom -types. - -
    Invalid atom type in molecule file - -
    Atom types must range from 1 to specified # of types. - -
    Invalid atom type in neighbor exclusion list - -
    Atom types must range from 1 to Ntypes inclusive. - -
    Invalid atom type index for fix shake - -
    Atom types must range from 1 to Ntypes inclusive. - -
    Invalid atom types in pair_write command - -
    Atom types must range from 1 to Ntypes inclusive. - -
    Invalid atom vector in variable formula - -
    The atom vector is not recognized. - -
    Invalid atom_style body command - -
    No body style argument was provided. - -
    Invalid atom_style command - -
    Self-explanatory. - -
    Invalid attribute in dump custom command - -
    Self-explantory. - -
    Invalid attribute in dump local command - -
    Self-explantory. - -
    Invalid attribute in dump modify command - -
    Self-explantory. - -
    Invalid basis setting in create_atoms command - -
    The basis index must be between 1 to N where N is the number of basis -atoms in the lattice. The type index must be between 1 to N where N -is the number of atom types. - -
    Invalid basis setting in fix append/atoms command - -
    The basis index must be between 1 to N where N is the number of basis -atoms in the lattice. The type index must be between 1 to N where N -is the number of atom types. - -
    Invalid bin bounds in compute chunk/atom - -
    The lo/hi values are inconsistent. - -
    Invalid bin bounds in fix ave/spatial - -
    The lo/hi values are inconsistent. - -
    Invalid body nparticle command - -
    Arguments in atom-style command are not correct. - -
    Invalid bond table length - -
    Length must be 2 or greater. - -
    Invalid bond type in Bonds section of data file - -
    Bond type must be positive integer and within range of specified bond -types. - -
    Invalid bond type in Bonds section of molecule file - -
    Self-explanatory. - -
    Invalid bond type in create_bonds command - -
    Self-explanatory. - -
    Invalid bond type in fix bond/break command - -
    Self-explanatory. - -
    Invalid bond type in fix bond/create command - -
    Self-explanatory. - -
    Invalid bond type index for fix shake - -
    Self-explanatory. Check the fix shake command in the input script. - -
    Invalid coeffs for this dihedral style - -
    Cannot set class 2 coeffs in data file for this dihedral style. - -
    Invalid color in dump_modify command - -
    The specified color name was not in the list of recognized colors. -See the dump_modify doc page. - -
    Invalid color map min/max values - -
    The min/max values are not consistent with either each other or -with values in the color map. - -
    Invalid command-line argument - -
    One or more command-line arguments is invalid. Check the syntax of -the command you are using to launch LAMMPS. - -
    Invalid compute ID in variable formula - -
    The compute is not recognized. - -
    Invalid create_atoms rotation vector for 2d model - -
    The rotation vector can only have a z component. - -
    Invalid custom OpenCL parameter string. - -
    There are not enough or too many parameters in the custom string for package -GPU. - -
    Invalid cutoff in comm_modify command - -
    Specified cutoff must be >= 0.0. - -
    Invalid cutoffs in pair_write command - -
    Inner cutoff must be larger than 0.0 and less than outer cutoff. - -
    Invalid d1 or d2 value for pair colloid coeff - -
    Neither d1 or d2 can be < 0. - -
    Invalid data file section: Angle Coeffs - -
    Atom style does not allow angles. - -
    Invalid data file section: AngleAngle Coeffs - -
    Atom style does not allow impropers. - -
    Invalid data file section: AngleAngleTorsion Coeffs - -
    Atom style does not allow dihedrals. - -
    Invalid data file section: AngleTorsion Coeffs - -
    Atom style does not allow dihedrals. - -
    Invalid data file section: Angles - -
    Atom style does not allow angles. - -
    Invalid data file section: Bodies - -
    Atom style does not allow bodies. - -
    Invalid data file section: Bond Coeffs - -
    Atom style does not allow bonds. - -
    Invalid data file section: BondAngle Coeffs - -
    Atom style does not allow angles. - -
    Invalid data file section: BondBond Coeffs - -
    Atom style does not allow angles. - -
    Invalid data file section: BondBond13 Coeffs - -
    Atom style does not allow dihedrals. - -
    Invalid data file section: Bonds - -
    Atom style does not allow bonds. - -
    Invalid data file section: Dihedral Coeffs - -
    Atom style does not allow dihedrals. - -
    Invalid data file section: Dihedrals - -
    Atom style does not allow dihedrals. - -
    Invalid data file section: Ellipsoids - -
    Atom style does not allow ellipsoids. - -
    Invalid data file section: EndBondTorsion Coeffs - -
    Atom style does not allow dihedrals. - -
    Invalid data file section: Improper Coeffs - -
    Atom style does not allow impropers. - -
    Invalid data file section: Impropers - -
    Atom style does not allow impropers. - -
    Invalid data file section: Lines - -
    Atom style does not allow lines. - -
    Invalid data file section: MiddleBondTorsion Coeffs - -
    Atom style does not allow dihedrals. - -
    Invalid data file section: Triangles - -
    Atom style does not allow triangles. - -
    Invalid delta_conf in tad command - -
    The value must be between 0 and 1 inclusive. - -
    Invalid density in Atoms section of data file - -
    Density value cannot be <= 0.0. - -
    Invalid density in set command - -
    Density must be > 0.0. - -
    Invalid diameter in set command - -
    Self-explanatory. - -
    Invalid dihedral type in Dihedrals section of data file - -
    Dihedral type must be positive integer and within range of specified -dihedral types. - -
    Invalid dihedral type in dihedrals section of molecule file - -
    Self-explanatory. - -
    Invalid dipole length in set command - -
    Self-explanatory. - -
    Invalid displace_atoms rotate axis for 2d - -
    Axis must be in z direction. - -
    Invalid dump dcd filename - -
    Filenames used with the dump dcd style cannot be binary or compressed -or cause multiple files to be written. - -
    Invalid dump frequency - -
    Dump frequency must be 1 or greater. - -
    Invalid dump image element name - -
    The specified element name was not in the standard list of elements. -See the dump_modify doc page. - -
    Invalid dump image filename - -
    The file produced by dump image cannot be binary and must -be for a single processor. - -
    Invalid dump image persp value - -
    Persp value must be >= 0.0. - -
    Invalid dump image theta value - -
    Theta must be between 0.0 and 180.0 inclusive. - -
    Invalid dump image zoom value - -
    Zoom value must be > 0.0. - -
    Invalid dump movie filename - -
    The file produced by dump movie cannot be binary or compressed -and must be a single file for a single processor. - -
    Invalid dump xtc filename - -
    Filenames used with the dump xtc style cannot be binary or compressed -or cause multiple files to be written. - -
    Invalid dump xyz filename - -
    Filenames used with the dump xyz style cannot be binary or cause files -to be written by each processor. - -
    Invalid dump_modify threshhold operator - -
    Operator keyword used for threshold specification in not recognized. - -
    Invalid entry in -reorder file - -
    Self-explanatory. - -
    Invalid fix ID in variable formula - -
    The fix is not recognized. - -
    Invalid fix ave/time off column - -
    Self-explantory. - -
    Invalid fix box/relax command for a 2d simulation - -
    Fix box/relax styles involving the z dimension cannot be used in -a 2d simulation. - -
    Invalid fix box/relax command pressure settings - -
    If multiple dimensions are coupled, those dimensions must be specified. - -
    Invalid fix box/relax pressure settings - -
    Settings for coupled dimensions must be the same. - -
    Invalid fix nvt/npt/nph command for a 2d simulation - -
    Cannot control z dimension in a 2d model. - -
    Invalid fix nvt/npt/nph command pressure settings - -
    If multiple dimensions are coupled, those dimensions must be -specified. - -
    Invalid fix nvt/npt/nph pressure settings - -
    Settings for coupled dimensions must be the same. - -
    Invalid fix press/berendsen for a 2d simulation - -
    The z component of pressure cannot be controlled for a 2d model. - -
    Invalid fix press/berendsen pressure settings - -
    Settings for coupled dimensions must be the same. - -
    Invalid fix qeq parameter file - -
    Element index > number of atom types. - -
    Invalid fix rigid npt/nph command for a 2d simulation - -
    Cannot control z dimension in a 2d model. - -
    Invalid fix rigid npt/nph command pressure settings - -
    If multiple dimensions are coupled, those dimensions must be -specified. - -
    Invalid fix rigid/small npt/nph command for a 2d simulation - -
    Cannot control z dimension in a 2d model. - -
    Invalid fix rigid/small npt/nph command pressure settings - -
    If multiple dimensions are coupled, those dimensions must be -specified. - -
    Invalid flag in force field section of restart file - -
    Unrecognized entry in restart file. - -
    Invalid flag in header section of restart file - -
    Unrecognized entry in restart file. - -
    Invalid flag in peratom section of restart file - -
    The format of this section of the file is not correct. - -
    Invalid flag in type arrays section of restart file - -
    Unrecognized entry in restart file. - -
    Invalid format in Bodies section of data file - -
    The specified number of integer or floating point values does not -appear. - -
    Invalid frequency in temper command - -
    Nevery must be > 0. - -
    Invalid group ID in neigh_modify command - -
    A group ID used in the neigh_modify command does not exist. - -
    Invalid group function in variable formula - -
    Group function is not recognized. - -
    Invalid group in comm_modify command - -
    Self-explanatory. - -
    Invalid image up vector - -
    Up vector cannot be (0,0,0). - -
    Invalid immediate variable - -
    Syntax of immediate value is incorrect. - -
    Invalid improper type in Impropers section of data file - -
    Improper type must be positive integer and within range of specified -improper types. - -
    Invalid improper type in impropers section of molecule file - -
    Self-explanatory. - -
    Invalid index for non-body particles in compute body/local command - -
    Only indices 1,2,3 can be used for non-body particles. - -
    Invalid index in compute body/local command - -
    Self-explanatory. - -
    Invalid keyword in angle table parameters - -
    Self-explanatory. - -
    Invalid keyword in bond table parameters - -
    Self-explanatory. - -
    Invalid keyword in compute angle/local command - -
    Self-explanatory. - -
    Invalid keyword in compute bond/local command - -
    Self-explanatory. - -
    Invalid keyword in compute dihedral/local command - -
    Self-explanatory. - -
    Invalid keyword in compute improper/local command - -
    Self-explanatory. - -
    Invalid keyword in compute pair/local command - -
    Self-explanatory. - -
    Invalid keyword in compute property/atom command - -
    Self-explanatory. - -
    Invalid keyword in compute property/chunk command - -
    Self-explanatory. - -
    Invalid keyword in compute property/local command - -
    Self-explanatory. - -
    Invalid keyword in dump cfg command - -
    Self-explanatory. - -
    Invalid keyword in pair table parameters - -
    Keyword used in list of table parameters is not recognized. - -
    Invalid length in set command - -
    Self-explanatory. - -
    Invalid mass in set command - -
    Self-explanatory. - -
    Invalid mass line in data file - -
    Self-explanatory. - -
    Invalid mass value - -
    Self-explanatory. - -
    Invalid math function in variable formula - -
    Self-explanatory. - -
    Invalid math/group/special function in variable formula - -
    Self-explanatory. - -
    Invalid option in lattice command for non-custom style - -
    Certain lattice keywords are not supported unless the -lattice style is "custom". - -
    Invalid order of forces within respa levels - -
    For respa, ordering of force computations within respa levels must -obey certain rules. E.g. bonds cannot be compute less frequently than -angles, pairwise forces cannot be computed less frequently than -kspace, etc. - -
    Invalid pair table cutoff - -
    Cutoffs in pair_coeff command are not valid with read-in pair table. - -
    Invalid pair table length - -
    Length of read-in pair table is invalid - -
    Invalid param file for fix qeq/shielded - -
    Invalid value of gamma. - -
    Invalid param file for fix qeq/slater - -
    Zeta value is 0.0. - -
    Invalid partitions in processors part command - -
    Valid partitions are numbered 1 to N and the sender and receiver -cannot be the same partition. - -
    Invalid python command - -
    Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -
    Invalid radius in Atoms section of data file - -
    Radius must be >= 0.0. - -
    Invalid random number seed in fix ttm command - -
    Random number seed must be > 0. - -
    Invalid random number seed in set command - -
    Random number seed must be > 0. - -
    Invalid replace values in compute reduce - -
    Self-explanatory. - -
    Invalid rigid body ID in fix rigid file - -
    The ID does not match the number of an existing ID of rigid bodies -that are defined by the fix rigid command. - -
    Invalid rigid body ID in fix rigid/small file - -
    The ID does not match the number of an existing ID of rigid bodies -that are defined by the fix rigid/small command. - -
    Invalid run command N value - -
    The number of timesteps must fit in a 32-bit integer. If you want to -run for more steps than this, perform multiple shorter runs. - -
    Invalid run command start/stop value - -
    Self-explanatory. - -
    Invalid run command upto value - -
    Self-explanatory. - -
    Invalid seed for Marsaglia random # generator - -
    The initial seed for this random number generator must be a positive -integer less than or equal to 900 million. - -
    Invalid seed for Park random # generator - -
    The initial seed for this random number generator must be a positive -integer. - -
    Invalid shake angle type in molecule file - -
    Self-explanatory. - -
    Invalid shake atom in molecule file - -
    Self-explanatory. - -
    Invalid shake bond type in molecule file - -
    Self-explanatory. - -
    Invalid shake flag in molecule file - -
    Self-explanatory. - -
    Invalid shape in Ellipsoids section of data file - -
    Self-explanatory. - -
    Invalid shape in Triangles section of data file - -
    Two or more of the triangle corners are duplicate points. - -
    Invalid shape in set command - -
    Self-explanatory. - -
    Invalid shear direction for fix wall/gran - -
    Self-explanatory. - -
    Invalid special atom index in molecule file - -
    Self-explanatory. - -
    Invalid special function in variable formula - -
    Self-explanatory. - -
    Invalid style in pair_write command - -
    Self-explanatory. Check the input script. - -
    Invalid syntax in variable formula - -
    Self-explanatory. - -
    Invalid t_event in prd command - -
    Self-explanatory. - -
    Invalid t_event in tad command - -
    The value must be greater than 0. - -
    Invalid template atom in Atoms section of data file - -
    The atom indices must be between 1 to N, where N is the number of -atoms in the template molecule the atom belongs to. - -
    Invalid template index in Atoms section of data file - -
    The template indices must be between 1 to N, where N is the number of -molecules in the template. - -
    Invalid thermo keyword in variable formula - -
    The keyword is not recognized. - -
    Invalid threads_per_atom specified. - -
    For 3-body potentials on the GPU, the threads_per_atom setting cannot be -greater than 4 for NVIDIA GPUs. - -
    Invalid timestep reset for fix ave/atom - -
    Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -
    Invalid timestep reset for fix ave/chunk - -
    Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -
    Invalid timestep reset for fix ave/correlate - -
    Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -
    Invalid timestep reset for fix ave/histo - -
    Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -
    Invalid timestep reset for fix ave/spatial - -
    Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -
    Invalid timestep reset for fix ave/time - -
    Resetting the timestep has invalidated the sequence of timesteps this -fix needs to process. - -
    Invalid tmax in tad command - -
    The value must be greater than 0.0. - -
    Invalid type for mass set - -
    Mass command must set a type from 1-N where N is the number of atom -types. - -
    Invalid use of library file() function - -
    This function is called thru the library interface. This -error should not occur. Contact the developers if it does. - -
    Invalid value in set command - -
    The value specified for the setting is invalid, likely because it is -too small or too large. - -
    Invalid variable evaluation in variable formula - -
    A variable used in a formula could not be evaluated. - -
    Invalid variable in next command - -
    Self-explanatory. - -
    Invalid variable name - -
    Variable name used in an input script line is invalid. - -
    Invalid variable name in variable formula - -
    Variable name is not recognized. - -
    Invalid variable style in special function next - -
    Only file-style or atomfile-style variables can be used with next(). - -
    Invalid variable style with next command - -
    Variable styles equal and world cannot be used in a next -command. - -
    Invalid volume in set command - -
    Volume must be > 0.0. - -
    Invalid wiggle direction for fix wall/gran - -
    Self-explanatory. - -
    Invoked angle equil angle on angle style none - -
    Self-explanatory. - -
    Invoked angle single on angle style none - -
    Self-explanatory. - -
    Invoked bond equil distance on bond style none - -
    Self-explanatory. - -
    Invoked bond single on bond style none - -
    Self-explanatory. - -
    Invoked pair single on pair style none - -
    A command (e.g. a dump) attempted to invoke the single() function on a -pair style none, which is illegal. You are probably attempting to -compute per-atom quantities with an undefined pair style. - -
    Invoking coulombic in pair style lj/coul requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Invoking coulombic in pair style lj/long/dipole/long requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    KIM neighbor iterator exceeded range - -
    This should not happen. It likely indicates a bug -in the KIM implementation of the interatomic potential -where it is requesting neighbors incorrectly. - -
    KOKKOS package does not yet support comm_style tiled - -
    Self-explanatory. - -
    KOKKOS package requires a kokkos enabled atom_style - -
    Self-explanatory. - -
    KSpace accuracy must be > 0 - -
    The kspace accuracy designated in the input must be greater than zero. - -
    KSpace accuracy too large to estimate G vector - -
    Reduce the accuracy request or specify gwald explicitly -via the kspace_modify command. - -
    KSpace accuracy too low - -
    Requested accuracy must be less than 1.0. - -
    KSpace solver requires a pair style - -
    No pair style is defined. - -
    KSpace style does not yet support triclinic geometries - -
    The specified kspace style does not allow for non-orthogonal -simulation boxes. - -
    KSpace style has not yet been set - -
    Cannot use kspace_modify command until a kspace style is set. - -
    KSpace style is incompatible with Pair style - -
    Setting a kspace style requires that a pair style with matching -long-range Coulombic or dispersion components be used. - -
    Keyword %s in MEAM parameter file not recognized - -
    Self-explanatory. - -
    Kspace style does not support compute group/group - -
    Self-explanatory. - -
    Kspace style pppm/disp/tip4p requires newton on - -
    Self-explanatory. - -
    Kspace style pppm/tip4p requires newton on - -
    Self-explanatory. - -
    Kspace style requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Kspace_modify eigtol must be smaller than one - -
    Self-explanatory. - -
    LAMMPS is not built with Python embedded - -
    This is done by including the PYTHON package before LAMMPS is built. -This is required to use python-style variables. - -
    LAMMPS unit_style lj not supported by KIM models - -
    Self-explanatory. Check the input script or data file. - -
    LJ6 off not supported in pair_style buck/long/coul/long - -
    Self-exlanatory. - -
    Label wasn't found in input script - -
    Self-explanatory. - -
    Lattice orient vectors are not orthogonal - -
    The three specified lattice orientation vectors must be mutually -orthogonal. - -
    Lattice orient vectors are not right-handed - -
    The three specified lattice orientation vectors must create a -right-handed coordinate system such that a1 cross a2 = a3. - -
    Lattice primitive vectors are collinear - -
    The specified lattice primitive vectors do not for a unit cell with -non-zero volume. - -
    Lattice settings are not compatible with 2d simulation - -
    One or more of the specified lattice vectors has a non-zero z -component. - -
    Lattice spacings are invalid - -
    Each x,y,z spacing must be > 0. - -
    Lattice style incompatible with simulation dimension - -
    2d simulation can use sq, sq2, or hex lattice. 3d simulation can use -sc, bcc, or fcc lattice. - -
    Log of zero/negative value in variable formula - -
    Self-explanatory. - -
    Lost atoms via balance: original %ld current %ld - -
    This should not occur. Report the problem to the developers. - -
    Lost atoms: original %ld current %ld - -
    Lost atoms are checked for each time thermo output is done. See the -thermo_modify lost command for options. Lost atoms usually indicate -bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before -reneighboring. - -
    MEAM library error %d - -
    A call to the MEAM Fortran library returned an error. - -
    MPI_LMP_BIGINT and bigint in lmptype.h are not compatible - -
    The size of the MPI datatype does not match the size of a bigint. - -
    MPI_LMP_TAGINT and tagint in lmptype.h are not compatible - -
    The size of the MPI datatype does not match the size of a tagint. - -
    MSM can only currently be used with comm_style brick - -
    This is a current restriction in LAMMPS. - -
    MSM grid is too large - -
    The global MSM grid is larger than OFFSET in one or more dimensions. -OFFSET is currently set to 16384. You likely need to decrease the -requested accuracy. - -
    MSM order must be 4, 6, 8, or 10 - -
    This is a limitation of the MSM implementation in LAMMPS: -the MSM order can only be 4, 6, 8, or 10. - -
    Mass command before simulation box is defined - -
    The mass command cannot be used before a read_data, read_restart, or -create_box command. - -
    Matrix factorization to split dispersion coefficients failed - -
    This should not normally happen. Contact the developers. - -
    Min_style command before simulation box is defined - -
    The min_style command cannot be used before a read_data, read_restart, -or create_box command. - -
    Minimization could not find thermo_pe compute - -
    This compute is created by the thermo command. It must have been -explicitly deleted by a uncompute command. - -
    Minimize command before simulation box is defined - -
    The minimize command cannot be used before a read_data, read_restart, -or create_box command. - -
    Mismatched brackets in variable - -
    Self-explanatory. - -
    Mismatched compute in variable formula - -
    A compute is referenced incorrectly or a compute that produces per-atom -values is used in an equal-style variable formula. - -
    Mismatched fix in variable formula - -
    A fix is referenced incorrectly or a fix that produces per-atom -values is used in an equal-style variable formula. - -
    Mismatched variable in variable formula - -
    A variable is referenced incorrectly or an atom-style variable that -produces per-atom values is used in an equal-style variable -formula. - -
    Modulo 0 in variable formula - -
    Self-explanatory. - -
    Molecule IDs too large for compute chunk/atom - -
    The IDs must not be larger than can be stored in a 32-bit integer -since chunk IDs are 32-bit integers. - -
    Molecule file has angles but no nangles setting - -
    Self-explanatory. - -
    Molecule file has bonds but no nbonds setting - -
    Self-explanatory. - -
    Molecule file has bonds but no special flags - -
    Self-explanatory. - -
    Molecule file has dihedrals but no ndihedrals setting - -
    Self-explanatory. - -
    Molecule file has impropers but no nimpropers setting - -
    Self-explanatory. - -
    Molecule file has special flags but no bonds - -
    Self-explanatory. - -
    Molecule file needs both Special Bond sections - -
    Self-explanatory. - -
    Molecule file shake flags not before shake atoms - -
    The order of the two sections is important. - -
    Molecule file shake flags not before shake bonds - -
    The order of the two sections is important. - -
    Molecule file shake info is incomplete - -
    All 3 SHAKE sections are needed. - -
    Molecule file special list does not match special count - -
    The number of values in an atom's special list does not match count. - -
    Molecule file z center-of-mass must be 0.0 for 2d - -
    Self-explanatory. - -
    Molecule file z coord must be 0.0 for 2d - -
    Self-explanatory. - -
    Molecule template ID for atom_style template does not exist - -
    Self-explanatory. - -
    Molecule template ID for create_atoms does not exist - -
    Self-explantory. - -
    Molecule template ID for fix deposit does not exist - -
    Self-explanatory. - -
    Molecule template ID for fix gcmc does not exist - -
    Self-explanatory. - -
    Molecule template ID for fix pour does not exist - -
    Self-explanatory. - -
    Molecule template ID for fix rigid/small does not exist - -
    Self-explanatory. - -
    Molecule template ID for fix shake does not exist - -
    Self-explanatory. - -
    Molecule template ID must be alphanumeric or underscore characters - -
    Self-explanatory. - -
    Molecule toplogy/atom exceeds system topology/atom - -
    The number of bonds, angles, etc per-atom in the molecule exceeds the -system setting. See the create_box command for how to specify these -values. - -
    Molecule topology type exceeds system topology type - -
    The number of bond, angle, etc types in the molecule exceeds the -system setting. See the create_box command for how to specify these -values. - -
    More than one fix deform - -
    Only one fix deform can be defined at a time. - -
    More than one fix freeze - -
    Only one of these fixes can be defined, since the granular pair -potentials access it. - -
    More than one fix shake - -
    Only one fix shake can be defined. - -
    Must define angle_style before Angle Coeffs - -
    Must use an angle_style command before reading a data file that -defines Angle Coeffs. - -
    Must define angle_style before BondAngle Coeffs - -
    Must use an angle_style command before reading a data file that -defines Angle Coeffs. - -
    Must define angle_style before BondBond Coeffs - -
    Must use an angle_style command before reading a data file that -defines Angle Coeffs. - -
    Must define bond_style before Bond Coeffs - -
    Must use a bond_style command before reading a data file that -defines Bond Coeffs. - -
    Must define dihedral_style before AngleAngleTorsion Coeffs - -
    Must use a dihedral_style command before reading a data file that -defines AngleAngleTorsion Coeffs. - -
    Must define dihedral_style before AngleTorsion Coeffs - -
    Must use a dihedral_style command before reading a data file that -defines AngleTorsion Coeffs. - -
    Must define dihedral_style before BondBond13 Coeffs - -
    Must use a dihedral_style command before reading a data file that -defines BondBond13 Coeffs. - -
    Must define dihedral_style before Dihedral Coeffs - -
    Must use a dihedral_style command before reading a data file that -defines Dihedral Coeffs. - -
    Must define dihedral_style before EndBondTorsion Coeffs - -
    Must use a dihedral_style command before reading a data file that -defines EndBondTorsion Coeffs. - -
    Must define dihedral_style before MiddleBondTorsion Coeffs - -
    Must use a dihedral_style command before reading a data file that -defines MiddleBondTorsion Coeffs. - -
    Must define improper_style before AngleAngle Coeffs - -
    Must use an improper_style command before reading a data file that -defines AngleAngle Coeffs. - -
    Must define improper_style before Improper Coeffs - -
    Must use an improper_style command before reading a data file that -defines Improper Coeffs. - -
    Must define pair_style before Pair Coeffs - -
    Must use a pair_style command before reading a data file that defines -Pair Coeffs. - -
    Must define pair_style before PairIJ Coeffs - -
    Must use a pair_style command before reading a data file that defines -PairIJ Coeffs. - -
    Must have more than one processor partition to temper - -
    Cannot use the temper command with only one processor partition. Use -the -partition command-line option. - -
    Must read Atoms before Angles - -
    The Atoms section of a data file must come before an Angles section. - -
    Must read Atoms before Bodies - -
    The Atoms section of a data file must come before a Bodies section. - -
    Must read Atoms before Bonds - -
    The Atoms section of a data file must come before a Bonds section. - -
    Must read Atoms before Dihedrals - -
    The Atoms section of a data file must come before a Dihedrals section. - -
    Must read Atoms before Ellipsoids - -
    The Atoms section of a data file must come before a Ellipsoids -section. - -
    Must read Atoms before Impropers - -
    The Atoms section of a data file must come before an Impropers -section. - -
    Must read Atoms before Lines - -
    The Atoms section of a data file must come before a Lines section. - -
    Must read Atoms before Triangles - -
    The Atoms section of a data file must come before a Triangles section. - -
    Must read Atoms before Velocities - -
    The Atoms section of a data file must come before a Velocities -section. - -
    Must set both respa inner and outer - -
    Cannot use just the inner or outer option with respa without using the -other. - -
    Must set number of threads via package omp command - -
    Because you are using the USER-OMP package, set the number of threads -via its settings, not by the pair_style snap nthreads setting. - -
    Must shrink-wrap piston boundary - -
    The boundary style of the face where the piston is applied must be of -type s (shrink-wrapped). - -
    Must specify a region in fix deposit - -
    The region keyword must be specified with this fix. - -
    Must specify a region in fix pour - -
    Self-explanatory. - -
    Must specify at least 2 types in fix atom/swap command - -
    Self-explanatory. - -
    Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM - -
    The kspace scalar pressure option cannot (yet) be used with rRESPA. - -
    Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm - -
    Otherwise MSM will compute only a scalar pressure. See the kspace_modify -command for details on this setting. - -
    Must use 'kspace_modify pressure/scalar no' to obtain per-atom virial with kspace_style MSM - -
    The kspace scalar pressure option cannot be used to obtain per-atom virial. - -
    Must use 'kspace_modify pressure/scalar no' with GPU MSM Pair styles - -
    The kspace scalar pressure option is not (yet) compatible with GPU MSM Pair styles. - -
    Must use 'kspace_modify pressure/scalar no' with kspace_style msm/cg - -
    The kspace scalar pressure option is not compatible with kspace_style msm/cg. - -
    Must use -in switch with multiple partitions - -
    A multi-partition simulation cannot read the input script from stdin. -The -in command-line option must be used to specify a file. - -
    Must use a block or cylinder region with fix pour - -
    Self-explanatory. - -
    Must use a block region with fix pour for 2d simulations - -
    Self-explanatory. - -
    Must use a bond style with TIP4P potential - -
    TIP4P potentials assume bond lengths in water are constrained -by a fix shake command. - -
    Must use a molecular atom style with fix poems molecule - -
    Self-explanatory. - -
    Must use a z-axis cylinder region with fix pour - -
    Self-explanatory. - -
    Must use an angle style with TIP4P potential - -
    TIP4P potentials assume angles in water are constrained by a fix shake -command. - -
    Must use atom map style array with Kokkos - -
    See the atom_modify map command. - -
    Must use atom style with molecule IDs with fix bond/swap - -
    Self-explanatory. - -
    Must use pair_style comb or comb3 with fix qeq/comb - -
    Self-explanatory. - -
    Must use variable energy with fix addforce - -
    Must define an energy vartiable when applyting a dynamic -force during minimization. - -
    Must use variable energy with fix efield - -
    You must define an energy when performing a minimization with a -variable E-field. - -
    NEB command before simulation box is defined - -
    Self-explanatory. - -
    NEB requires damped dynamics minimizer - -
    Use a different minimization style. - -
    NEB requires use of fix neb - -
    Self-explanatory. - -
    NL ramp in wall/piston only implemented in zlo for now - -
    The ramp keyword can only be used for piston applied to face zlo. - -
    Need ntypes-1 delta_mu values in fix atom/swap command - -
    Self-explanatory. - -
    Needed bonus data not in data file - -
    Some atom styles require bonus data. See the read_data doc page for -details. - -
    Needed molecular topology not in data file - -
    The header of the data file indicated bonds, angles, etc would be -included, but they are not present. - -
    Neigh_modify exclude molecule requires atom attribute molecule - -
    Self-explanatory. - -
    Neigh_modify include group != atom_modify first group - -
    Self-explanatory. - -
    Neighbor delay must be 0 or multiple of every setting - -
    The delay and every parameters set via the neigh_modify command are -inconsistent. If the delay setting is non-zero, then it must be a -multiple of the every setting. - -
    Neighbor include group not allowed with ghost neighbors - -
    This is a current restriction within LAMMPS. - -
    Neighbor list overflow, boost neigh_modify one - -
    There are too many neighbors of a single atom. Use the neigh_modify -command to increase the max number of neighbors allowed for one atom. -You may also want to boost the page size. - -
    Neighbor multi not yet enabled for ghost neighbors - -
    This is a current restriction within LAMMPS. - -
    Neighbor multi not yet enabled for granular - -
    Self-explanatory. - -
    Neighbor multi not yet enabled for rRESPA - -
    Self-explanatory. - -
    Neighbor page size must be >= 10x the one atom setting - -
    This is required to prevent wasting too much memory. - -
    New atom IDs exceed maximum allowed ID - -
    See the setting for tagint in the src/lmptype.h file. - -
    New bond exceeded bonds per atom in create_bonds - -
    See the read_data command for info on setting the "extra bond per -atom" header value to allow for additional bonds to be formed. - -
    New bond exceeded bonds per atom in fix bond/create - -
    See the read_data command for info on setting the "extra bond per -atom" header value to allow for additional bonds to be formed. - -
    New bond exceeded special list size in fix bond/create - -
    See the special_bonds extra command for info on how to leave space in -the special bonds list to allow for additional bonds to be formed. - -
    Newton bond change after simulation box is defined - -
    The newton command cannot be used to change the newton bond value -after a read_data, read_restart, or create_box command. - -
    Next command must list all universe and uloop variables - -
    This is to insure they stay in sync. - -
    No Kspace style defined for compute group/group - -
    Self-explanatory. - -
    No OpenMP support compiled in - -
    An OpenMP flag is set, but LAMMPS was not built with -OpenMP support. - -
    No angle style is defined for compute angle/local - -
    Self-explanatory. - -
    No angles allowed with this atom style - -
    Self-explanatory. - -
    No atom count in molecule file - -
    Self-explanatory. - -
    No atoms in data file - -
    The header of the data file indicated that atoms would be included, -but they are not present. - -
    No basis atoms in lattice - -
    Basis atoms must be defined for lattice style user. - -
    No bodies allowed with this atom style - -
    Self-explanatory. Check data file. - -
    No bond style is defined for compute bond/local - -
    Self-explanatory. - -
    No bonds allowed with this atom style - -
    Self-explanatory. - -
    No box information in dump. You have to use 'box no' - -
    Self-explanatory. - -
    No dihedral style is defined for compute dihedral/local - -
    Self-explanatory. - -
    No dihedrals allowed with this atom style - -
    Self-explanatory. - -
    No dump custom arguments specified - -
    The dump custom command requires that atom quantities be specified to -output to dump file. - -
    No dump local arguments specified - -
    Self-explanatory. - -
    No ellipsoids allowed with this atom style - -
    Self-explanatory. Check data file. - -
    No fix gravity defined for fix pour - -
    Gravity is required to use fix pour. - -
    No improper style is defined for compute improper/local - -
    Self-explanatory. - -
    No impropers allowed with this atom style - -
    Self-explanatory. - -
    No input values for fix ave/spatial - -
    Self-explanatory. - -
    No lines allowed with this atom style - -
    Self-explanatory. Check data file. - -
    No matching element in ADP potential file - -
    The ADP potential file does not contain elements that match the -requested elements. - -
    No matching element in EAM potential file - -
    The EAM potential file does not contain elements that match the -requested elements. - -
    No molecule topology allowed with atom style template - -
    The data file cannot specify the number of bonds, angles, etc, -because this info if inferred from the molecule templates. - -
    No overlap of box and region for create_atoms - -
    Self-explanatory. - -
    No pair coul/streitz for fix qeq/slater - -
    These commands must be used together. - -
    No pair hbond/dreiding coefficients set - -
    Self-explanatory. - -
    No pair style defined for compute group/group - -
    Cannot calculate group interactions without a pair style defined. - -
    No pair style is defined for compute pair/local - -
    Self-explanatory. - -
    No pair style is defined for compute property/local - -
    Self-explanatory. - -
    No rigid bodies defined - -
    The fix specification did not end up defining any rigid bodies. - -
    No triangles allowed with this atom style - -
    Self-explanatory. Check data file. - -
    Non digit character between brackets in variable - -
    Self-explantory. - -
    Non integer # of swaps in temper command - -
    Swap frequency in temper command must evenly divide the total # of -timesteps. - -
    Non-numeric box dimensions - simulation unstable - -
    The box size has apparently blown up. - -
    Not all atom IDs are 0 - -
    Either all atoms IDs must be zero or none of them. - -
    Nprocs not a multiple of N for -reorder - -
    Self-explanatory. - -
    Number of core atoms != number of shell atoms - -
    There must be a one-to-one pairing of core and shell atoms. - -
    Numeric index is out of bounds - -
    A command with an argument that specifies an integer or range of -integers is using a value that is less than 1 or greater than the -maximum allowed limit. - -
    One or more atoms belong to multiple rigid bodies - -
    Two or more rigid bodies defined by the fix rigid command cannot -contain the same atom. - -
    One or zero atoms in rigid body - -
    Any rigid body defined by the fix rigid command must contain 2 or more -atoms. - -
    Only 2 types allowed when not using semi-grand in fix atom/swap command - -
    Self-explanatory. - -
    Only one cut-off allowed when requesting all long - -
    Self-explanatory. - -
    Only one cutoff allowed when requesting all long - -
    Self-explanatory. - -
    Only zhi currently implemented for fix append/atoms - -
    Self-explanatory. - -
    Out of range atoms - cannot compute MSM - -
    One or more atoms are attempting to map their charge to a MSM grid point -that is not owned by a processor. This is likely for one of two -reasons, both of them bad. First, it may mean that an atom near the -boundary of a processor's sub-domain has moved more than 1/2 the -neighbor skin distance without neighbor lists being -rebuilt and atoms being migrated to new processors. This also means -you may be missing pairwise interactions that need to be computed. -The solution is to change the re-neighboring criteria via the -neigh_modify command. The safest settings are "delay 0 -every 1 check yes". Second, it may mean that an atom has moved far -outside a processor's sub-domain or even the entire simulation box. -This indicates bad physics, e.g. due to highly overlapping atoms, too -large a timestep, etc. - -
    Out of range atoms - cannot compute PPPM - -
    One or more atoms are attempting to map their charge to a PPPM grid -point that is not owned by a processor. This is likely for one of two -reasons, both of them bad. First, it may mean that an atom near the -boundary of a processor's sub-domain has moved more than 1/2 the -neighbor skin distance without neighbor lists being -rebuilt and atoms being migrated to new processors. This also means -you may be missing pairwise interactions that need to be computed. -The solution is to change the re-neighboring criteria via the -neigh_modify command. The safest settings are "delay 0 -every 1 check yes". Second, it may mean that an atom has moved far -outside a processor's sub-domain or even the entire simulation box. -This indicates bad physics, e.g. due to highly overlapping atoms, too -large a timestep, etc. - -
    Out of range atoms - cannot compute PPPMDisp - -
    One or more atoms are attempting to map their charge to a PPPM grid -point that is not owned by a processor. This is likely for one of two -reasons, both of them bad. First, it may mean that an atom near the -boundary of a processor's sub-domain has moved more than 1/2 the -neighbor skin distance without neighbor lists being -rebuilt and atoms being migrated to new processors. This also means -you may be missing pairwise interactions that need to be computed. -The solution is to change the re-neighboring criteria via the -neigh_modify command. The safest settings are "delay 0 -every 1 check yes". Second, it may mean that an atom has moved far -outside a processor's sub-domain or even the entire simulation box. -This indicates bad physics, e.g. due to highly overlapping atoms, too -large a timestep, etc. - -
    Overflow of allocated fix vector storage - -
    This should not normally happen if the fix correctly calculated -how long the vector will grow to. Contact the developers. - -
    Overlapping large/large in pair colloid - -
    This potential is infinite when there is an overlap. - -
    Overlapping small/large in pair colloid - -
    This potential is infinite when there is an overlap. - -
    POEMS fix must come before NPT/NPH fix - -
    NPT/NPH fix must be defined in input script after all poems fixes, -else the fix contribution to the pressure virial is incorrect. - -
    PPPM can only currently be used with comm_style brick - -
    This is a current restriction in LAMMPS. - -
    PPPM grid is too large - -
    The global PPPM grid is larger than OFFSET in one or more dimensions. -OFFSET is currently set to 4096. You likely need to decrease the -requested accuracy. - -
    PPPM grid stencil extends beyond nearest neighbor processor - -
    This is not allowed if the kspace_modify overlap setting is no. - -
    PPPM order < minimum allowed order - -
    The default minimum order is 2. This can be reset by the -kspace_modify minorder command. - -
    PPPM order cannot be < 2 or > than %d - -
    This is a limitation of the PPPM implementation in LAMMPS. - -
    PPPMDisp Coulomb grid is too large - -
    The global PPPM grid is larger than OFFSET in one or more dimensions. -OFFSET is currently set to 4096. You likely need to decrease the -requested accuracy. - -
    PPPMDisp Dispersion grid is too large - -
    The global PPPM grid is larger than OFFSET in one or more dimensions. -OFFSET is currently set to 4096. You likely need to decrease the -requested accuracy. - -
    PPPMDisp can only currently be used with comm_style brick - -
    This is a current restriction in LAMMPS. - -
    PPPMDisp coulomb order cannot be greater than %d - -
    This is a limitation of the PPPM implementation in LAMMPS. - -
    PPPMDisp used but no parameters set, for further information please see the pppm/disp documentation - -
    An efficient and accurate usage of the pppm/disp requires settings via the kspace_modify command. Please see the pppm/disp documentation for further instructions. - -
    PRD command before simulation box is defined - -
    The prd command cannot be used before a read_data, -read_restart, or create_box command. - -
    PRD nsteps must be multiple of t_event - -
    Self-explanatory. - -
    PRD t_corr must be multiple of t_event - -
    Self-explanatory. - -
    Package command after simulation box is defined - -
    The package command cannot be used afer a read_data, read_restart, or -create_box command. - -
    Package cuda command without USER-CUDA package enabled - -
    The USER-CUDA package must be installed via "make yes-user-cuda" -before LAMMPS is built, and the "-c on" must be used to enable the -package. - -
    Package gpu command without GPU package installed - -
    The GPU package must be installed via "make yes-gpu" before LAMMPS is -built. - -
    Package intel command without USER-INTEL package installed - -
    The USER-INTEL package must be installed via "make yes-user-intel" -before LAMMPS is built. - -
    Package kokkos command without KOKKOS package enabled - -
    The KOKKOS package must be installed via "make yes-kokkos" before -LAMMPS is built, and the "-k on" must be used to enable the package. - -
    Package omp command without USER-OMP package installed - -
    The USER-OMP package must be installed via "make yes-user-omp" before -LAMMPS is built. - -
    Pair body requires atom style body - -
    Self-explanatory. - -
    Pair body requires body style nparticle - -
    This pair style is specific to the nparticle body style. - -
    Pair brownian requires atom style sphere - -
    Self-explanatory. - -
    Pair brownian requires extended particles - -
    One of the particles has radius 0.0. - -
    Pair brownian requires monodisperse particles - -
    All particles must be the same finite size. - -
    Pair brownian/poly requires atom style sphere - -
    Self-explanatory. - -
    Pair brownian/poly requires extended particles - -
    One of the particles has radius 0.0. - -
    Pair brownian/poly requires newton pair off - -
    Self-explanatory. - -
    Pair coeff for hybrid has invalid style - -
    Style in pair coeff must have been listed in pair_style command. - -
    Pair coul/wolf requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair cutoff < Respa interior cutoff - -
    One or more pairwise cutoffs are too short to use with the specified -rRESPA cutoffs. - -
    Pair dipole/cut requires atom attributes q, mu, torque - -
    The atom style defined does not have these attributes. - -
    Pair dipole/cut/gpu requires atom attributes q, mu, torque - -
    The atom style defined does not have this attribute. - -
    Pair dipole/long requires atom attributes q, mu, torque - -
    The atom style defined does not have these attributes. - -
    Pair distance < table inner cutoff - -
    Two atoms are closer together than the pairwise table allows. - -
    Pair distance > table outer cutoff - -
    Two atoms are further apart than the pairwise table allows. - -
    Pair dpd requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Pair gayberne epsilon a,b,c coeffs are not all set - -
    Each atom type involved in pair_style gayberne must -have these 3 coefficients set at least once. - -
    Pair gayberne requires atom style ellipsoid - -
    Self-explanatory. - -
    Pair gayberne requires atoms with same type have same shape - -
    Self-explanatory. - -
    Pair gayberne/gpu requires atom style ellipsoid - -
    Self-explanatory. - -
    Pair gayberne/gpu requires atoms with same type have same shape - -
    Self-explanatory. - -
    Pair granular requires atom style sphere - -
    Self-explanatory. - -
    Pair granular requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Pair granular with shear history requires newton pair off - -
    This is a current restriction of the implementation of pair -granular styles with history. - -
    Pair hybrid sub-style does not support single call - -
    You are attempting to invoke a single() call on a pair style -that doesn't support it. - -
    Pair hybrid sub-style is not used - -
    No pair_coeff command used a sub-style specified in the pair_style -command. - -
    Pair inner cutoff < Respa interior cutoff - -
    One or more pairwise cutoffs are too short to use with the specified -rRESPA cutoffs. - -
    Pair inner cutoff >= Pair outer cutoff - -
    The specified cutoffs for the pair style are inconsistent. - -
    Pair line/lj requires atom style line - -
    Self-explanatory. - -
    Pair lj/long/dipole/long requires atom attributes mu, torque - -
    The atom style defined does not have these attributes. - -
    Pair lubricate requires atom style sphere - -
    Self-explanatory. - -
    Pair lubricate requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Pair lubricate requires monodisperse particles - -
    All particles must be the same finite size. - -
    Pair lubricate/poly requires atom style sphere - -
    Self-explanatory. - -
    Pair lubricate/poly requires extended particles - -
    One of the particles has radius 0.0. - -
    Pair lubricate/poly requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Pair lubricate/poly requires newton pair off - -
    Self-explanatory. - -
    Pair lubricateU requires atom style sphere - -
    Self-explanatory. - -
    Pair lubricateU requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Pair lubricateU requires monodisperse particles - -
    All particles must be the same finite size. - -
    Pair lubricateU/poly requires ghost atoms store velocity - -
    Use the comm_modify vel yes command to enable this. - -
    Pair lubricateU/poly requires newton pair off - -
    Self-explanatory. - -
    Pair peri lattice is not identical in x, y, and z - -
    The lattice defined by the lattice command must be cubic. - -
    Pair peri requires a lattice be defined - -
    Use the lattice command for this purpose. - -
    Pair peri requires an atom map, see atom_modify - -
    Even for atomic systems, an atom map is required to find Peridynamic -bonds. Use the atom_modify command to define one. - -
    Pair resquared epsilon a,b,c coeffs are not all set - -
    Self-explanatory. - -
    Pair resquared epsilon and sigma coeffs are not all set - -
    Self-explanatory. - -
    Pair resquared requires atom style ellipsoid - -
    Self-explanatory. - -
    Pair resquared requires atoms with same type have same shape - -
    Self-explanatory. - -
    Pair resquared/gpu requires atom style ellipsoid - -
    Self-explanatory. - -
    Pair resquared/gpu requires atoms with same type have same shape - -
    Self-explanatory. - -
    Pair style AIREBO requires atom IDs - -
    This is a requirement to use the AIREBO potential. - -
    Pair style AIREBO requires newton pair on - -
    See the newton command. This is a restriction to use the AIREBO -potential. - -
    Pair style BOP requires atom IDs - -
    This is a requirement to use the BOP potential. - -
    Pair style BOP requires newton pair on - -
    See the newton command. This is a restriction to use the BOP -potential. - -
    Pair style COMB requires atom IDs - -
    This is a requirement to use the AIREBO potential. - -
    Pair style COMB requires atom attribute q - -
    Self-explanatory. - -
    Pair style COMB requires newton pair on - -
    See the newton command. This is a restriction to use the COMB -potential. - -
    Pair style COMB3 requires atom IDs - -
    This is a requirement to use the COMB3 potential. - -
    Pair style COMB3 requires atom attribute q - -
    Self-explanatory. - -
    Pair style COMB3 requires newton pair on - -
    See the newton command. This is a restriction to use the COMB3 -potential. - -
    Pair style LCBOP requires atom IDs - -
    This is a requirement to use the LCBOP potential. - -
    Pair style LCBOP requires newton pair on - -
    See the newton command. This is a restriction to use the Tersoff -potential. - -
    Pair style MEAM requires newton pair on - -
    See the newton command. This is a restriction to use the MEAM -potential. - -
    Pair style SNAP requires newton pair on - -
    See the newton command. This is a restriction to use the SNAP -potential. - -
    Pair style Stillinger-Weber requires atom IDs - -
    This is a requirement to use the SW potential. - -
    Pair style Stillinger-Weber requires newton pair on - -
    See the newton command. This is a restriction to use the SW -potential. - -
    Pair style Tersoff requires atom IDs - -
    This is a requirement to use the Tersoff potential. - -
    Pair style Tersoff requires newton pair on - -
    See the newton command. This is a restriction to use the Tersoff -potential. - -
    Pair style bop requires comm ghost cutoff at least 3x larger than %g - -
    Use the communicate ghost command to set this. See the pair bop -doc page for more details. - -
    Pair style born/coul/long requires atom attribute q - -
    An atom style that defines this attribute must be used. - -
    Pair style born/coul/long/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style born/coul/wolf requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style buck/coul/cut requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style buck/coul/long requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style buck/coul/long/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style buck/long/coul/long requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style coul/cut requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style coul/cut/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style coul/debye/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style coul/dsf requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style coul/dsf/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style coul/long/gpu requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style coul/streitz requires atom attribute q - -
    Self-explanatory. - -
    Pair style does not have extra field requested by compute pair/local - -
    The pair style does not support the pN value requested by the compute -pair/local command. - -
    Pair style does not support bond_style quartic - -
    The pair style does not have a single() function, so it can -not be invoked by bond_style quartic. - -
    Pair style does not support compute group/group - -
    The pair_style does not have a single() function, so it cannot be -invokded by the compute group/group command. - -
    Pair style does not support compute pair/local - -
    The pair style does not have a single() function, so it can -not be invoked by compute pair/local. - -
    Pair style does not support compute property/local - -
    The pair style does not have a single() function, so it can -not be invoked by fix bond/swap. - -
    Pair style does not support fix bond/swap - -
    The pair style does not have a single() function, so it can -not be invoked by fix bond/swap. - -
    Pair style does not support pair_write - -
    The pair style does not have a single() function, so it can -not be invoked by pair write. - -
    Pair style does not support rRESPA inner/middle/outer - -
    You are attempting to use rRESPA options with a pair style that -does not support them. - -
    Pair style granular with history requires atoms have IDs - -
    Atoms in the simulation do not have IDs, so history effects -cannot be tracked by the granular pair potential. - -
    Pair style hbond/dreiding requires an atom map, see atom_modify - -
    Self-explanatory. - -
    Pair style hbond/dreiding requires atom IDs - -
    Self-explanatory. - -
    Pair style hbond/dreiding requires molecular system - -
    Self-explanatory. - -
    Pair style hbond/dreiding requires newton pair on - -
    See the newton command for details. - -
    Pair style hybrid cannot have hybrid as an argument - -
    Self-explanatory. - -
    Pair style hybrid cannot have none as an argument - -
    Self-explanatory. - -
    Pair style is incompatible with TIP4P KSpace style - -
    The pair style does not have the requires TIP4P settings. - -
    Pair style lj/charmm/coul/charmm requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style lj/charmm/coul/long requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style lj/charmm/coul/long/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/class2/coul/cut requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/class2/coul/long requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/class2/coul/long/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/coul/cut requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/coul/cut/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/coul/debye/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/coul/dsf requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style lj/cut/coul/dsf/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/coul/long requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/coul/long/gpu requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/tip4p/cut requires atom IDs - -
    This is a requirement to use this potential. - -
    Pair style lj/cut/tip4p/cut requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style lj/cut/tip4p/cut requires newton pair on - -
    See the newton command. This is a restriction to use this -potential. - -
    Pair style lj/cut/tip4p/long requires atom IDs - -
    There are no atom IDs defined in the system and the TIP4P potential -requires them to find O,H atoms with a water molecule. - -
    Pair style lj/cut/tip4p/long requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style lj/cut/tip4p/long requires newton pair on - -
    This is because the computation of constraint forces within a water -molecule adds forces to atoms owned by other processors. - -
    Pair style lj/gromacs/coul/gromacs requires atom attribute q - -
    An atom_style with this attribute is needed. - -
    Pair style lj/long/dipole/long does not currently support respa - -
    This feature is not yet supported. - -
    Pair style lj/long/tip4p/long requires atom IDs - -
    There are no atom IDs defined in the system and the TIP4P potential -requires them to find O,H atoms with a water molecule. - -
    Pair style lj/long/tip4p/long requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style lj/long/tip4p/long requires newton pair on - -
    This is because the computation of constraint forces within a water -molecule adds forces to atoms owned by other processors. - -
    Pair style nb3b/harmonic requires atom IDs - -
    This is a requirement to use this potential. - -
    Pair style nb3b/harmonic requires newton pair on - -
    See the newton command. This is a restriction to use this potential. - -
    Pair style nm/cut/coul/cut requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style nm/cut/coul/long requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style peri requires atom style peri - -
    Self-explanatory. - -
    Pair style reax requires atom IDs - -
    This is a requirement to use the ReaxFF potential. - -
    Pair style reax requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style reax requires newton pair on - -
    This is a requirement to use the ReaxFF potential. - -
    Pair style requires a KSpace style - -
    No kspace style is defined. - -
    Pair style requires use of kspace_style ewald/disp - -
    Self-explanatory. - -
    Pair style sw/gpu requires atom IDs - -
    This is a requirement to use this potential. - -
    Pair style sw/gpu requires newton pair off - -
    See the newton command. This is a restriction to use this potential. - -
    Pair style tip4p/cut requires atom IDs - -
    This is a requirement to use this potential. - -
    Pair style tip4p/cut requires atom attribute q - -
    The atom style defined does not have this attribute. - -
    Pair style tip4p/cut requires newton pair on - -
    See the newton command. This is a restriction to use this potential. - -
    Pair style tip4p/long requires atom IDs - -
    There are no atom IDs defined in the system and the TIP4P potential -requires them to find O,H atoms with a water molecule. - -
    Pair style tip4p/long requires atom attribute q - -
    The atom style defined does not have these attributes. - -
    Pair style tip4p/long requires newton pair on - -
    This is because the computation of constraint forces within a water -molecule adds forces to atoms owned by other processors. - -
    Pair table cutoffs must all be equal to use with KSpace - -
    When using pair style table with a long-range KSpace solver, the -cutoffs for all atom type pairs must all be the same, since the -long-range solver starts at that cutoff. - -
    Pair table parameters did not set N - -
    List of pair table parameters must include N setting. - -
    Pair tersoff/zbl requires metal or real units - -
    This is a current restriction of this pair potential. - -
    Pair tri/lj requires atom style tri - -
    Self-explanatory. - -
    Pair yukawa/colloid requires atom style sphere - -
    Self-explantory. - -
    Pair yukawa/colloid requires atoms with same type have same radius - -
    Self-explantory. - -
    Pair yukawa/colloid/gpu requires atom style sphere - -
    Self-explanatory. - -
    PairKIM only works with 3D problems - -
    This is a current limitation. - -
    Pair_coeff command before pair_style is defined - -
    Self-explanatory. - -
    Pair_coeff command before simulation box is defined - -
    The pair_coeff command cannot be used before a read_data, -read_restart, or create_box command. - -
    Pair_modify command before pair_style is defined - -
    Self-explanatory. - -
    Pair_write command before pair_style is defined - -
    Self-explanatory. - -
    Particle on or inside fix wall surface - -
    Particles must be "exterior" to the wall in order for energy/force to -be calculated. - -
    Particle on or inside surface of region used in fix wall/region - -
    Particles must be "exterior" to the region surface in order for -energy/force to be calculated. - -
    Per-atom compute in equal-style variable formula - -
    Equal-style variables cannot use per-atom quantities. - -
    Per-atom energy was not tallied on needed timestep - -
    You are using a thermo keyword that requires potentials to -have tallied energy, but they didn't on this timestep. See the -variable doc page for ideas on how to make this work. - -
    Per-atom fix in equal-style variable formula - -
    Equal-style variables cannot use per-atom quantities. - -
    Per-atom virial was not tallied on needed timestep - -
    You are using a thermo keyword that requires potentials to have -tallied the virial, but they didn't on this timestep. See the -variable doc page for ideas on how to make this work. - -
    Per-processor system is too big - -
    The number of owned atoms plus ghost atoms on a single -processor must fit in 32-bit integer. - -
    Potential energy ID for fix neb does not exist - -
    Self-explanatory. - -
    Potential energy ID for fix nvt/nph/npt does not exist - -
    A compute for potential energy must be defined. - -
    Potential file has duplicate entry - -
    The potential file has more than one entry for the same element. - -
    Potential file is missing an entry - -
    The potential file does not have a needed entry. - -
    Power by 0 in variable formula - -
    Self-explanatory. - -
    Pressure ID for fix box/relax does not exist - -
    The compute ID needed to compute pressure for the fix does not -exist. - -
    Pressure ID for fix modify does not exist - -
    Self-explanatory. - -
    Pressure ID for fix npt/nph does not exist - -
    Self-explanatory. - -
    Pressure ID for fix press/berendsen does not exist - -
    The compute ID needed to compute pressure for the fix does not -exist. - -
    Pressure ID for fix rigid npt/nph does not exist - -
    Self-explanatory. - -
    Pressure ID for thermo does not exist - -
    The compute ID needed to compute pressure for thermodynamics does not -exist. - -
    Pressure control can not be used with fix nvt - -
    Self-explanatory. - -
    Pressure control can not be used with fix nvt/asphere - -
    Self-explanatory. - -
    Pressure control can not be used with fix nvt/sllod - -
    Self-explanatory. - -
    Pressure control can not be used with fix nvt/sphere - -
    Self-explanatory. - -
    Pressure control must be used with fix nph - -
    Self-explanatory. - -
    Pressure control must be used with fix nph/asphere - -
    Self-explanatory. - -
    Pressure control must be used with fix nph/small - -
    Self-explanatory. - -
    Pressure control must be used with fix nph/sphere - -
    Self-explanatory. - -
    Pressure control must be used with fix nphug - -
    A pressure control keyword (iso, aniso, tri, x, y, or z) must be -provided. - -
    Pressure control must be used with fix npt - -
    Self-explanatory. - -
    Pressure control must be used with fix npt/asphere - -
    Self-explanatory. - -
    Pressure control must be used with fix npt/sphere - -
    Self-explanatory. - -
    Processor count in z must be 1 for 2d simulation - -
    Self-explanatory. - -
    Processor partitions do not match number of allocated processors - -
    The total number of processors in all partitions must match the number -of processors LAMMPS is running on. - -
    Processors command after simulation box is defined - -
    The processors command cannot be used after a read_data, read_restart, -or create_box command. - -
    Processors custom grid file is inconsistent - -
    The vales in the custom file are not consistent with the number of -processors you are running on or the Px,Py,Pz settings of the -processors command. Or there was not a setting for every processor. - -
    Processors grid numa and map style are incompatible - -
    Using numa for gstyle in the processors command requires using -cart for the map option. - -
    Processors part option and grid style are incompatible - -
    Cannot use gstyle numa or custom with the part option. - -
    Processors twogrid requires proc count be a multiple of core count - -
    Self-explanatory. - -
    Pstart and Pstop must have the same value - -
    Self-explanatory. - -
    Python function evaluation failed - -
    The Python function did not run succesfully and/or did not return a -value (if it is supposed to return a value). This is probably due to -some error condition in the function. - -
    Python function is not callable - -
    The provided Python code was run successfully, but it not -define a callable function with the required name. - -
    Python invoke of undefined function - -
    Cannot invoke a function that has not been previously defined. - -
    Python variable does not match Python function - -
    This matching is defined by the python-style variable and the python -command. - -
    Python variable has no function - -
    No python command was used to define the function associated with the -python-style variable. - -
    QEQ with 'newton pair off' not supported - -
    See the newton command. This is a restriction to use the QEQ fixes. - -
    R0 < 0 for fix spring command - -
    Equilibrium spring length is invalid. - -
    RATTLE coordinate constraints are not satisfied up to desired tolerance - -
    Self-explanatory. - -
    RATTLE determinant = 0.0 - -
    The determinant of the matrix being solved for a single cluster -specified by the fix rattle command is numerically invalid. - -
    RATTLE failed - -
    Certain constraints were not satisfied. - -
    RATTLE velocity constraints are not satisfied up to desired tolerance - -
    Self-explanatory. - -
    Read dump of atom property that isn't allocated - -
    Self-explanatory. - -
    Read rerun dump file timestep > specified stop - -
    Self-explanatory. - -
    Read restart MPI-IO input not allowed with % in filename - -
    This is because a % signifies one file per processor and MPI-IO -creates one large file for all processors. - -
    Read_data shrink wrap did not assign all atoms correctly - -
    This is typically because the box-size specified in the data file is -large compared to the actual extent of atoms in a shrink-wrapped -dimension. When LAMMPS shrink-wraps the box atoms will be lost if the -processor they are re-assigned to is too far away. Choose a box -size closer to the actual extent of the atoms. - -
    Read_dump command before simulation box is defined - -
    The read_dump command cannot be used before a read_data, read_restart, -or create_box command. - -
    Read_dump field not found in dump file - -
    Self-explanatory. - -
    Read_dump triclinic status does not match simulation - -
    Both the dump snapshot and the current LAMMPS simulation must -be using either an orthogonal or triclinic box. - -
    Read_dump xyz fields do not have consistent scaling/wrapping - -
    Self-explanatory. - -
    Reading from MPI-IO filename when MPIIO package is not installed - -
    Self-explanatory. - -
    Reax_defs.h setting for NATDEF is too small - -
    Edit the setting in the ReaxFF library and re-compile the -library and re-build LAMMPS. - -
    Reax_defs.h setting for NNEIGHMAXDEF is too small - -
    Edit the setting in the ReaxFF library and re-compile the -library and re-build LAMMPS. - -
    Receiving partition in processors part command is already a receiver - -
    Cannot specify a partition to be a receiver twice. - -
    Region ID for compute chunk/atom does not exist - -
    Self-explanatory. - -
    Region ID for compute reduce/region does not exist - -
    Self-explanatory. - -
    Region ID for compute temp/region does not exist - -
    Self-explanatory. - -
    Region ID for dump custom does not exist - -
    Self-explanatory. - -
    Region ID for fix addforce does not exist - -
    Self-explanatory. - -
    Region ID for fix atom/swap does not exist - -
    Self-explanatory. - -
    Region ID for fix ave/spatial does not exist - -
    Self-explanatory. - -
    Region ID for fix aveforce does not exist - -
    Self-explanatory. - -
    Region ID for fix deposit does not exist - -
    Self-explanatory. - -
    Region ID for fix efield does not exist - -
    Self-explanatory. - -
    Region ID for fix evaporate does not exist - -
    Self-explanatory. - -
    Region ID for fix gcmc does not exist - -
    Self-explanatory. - -
    Region ID for fix heat does not exist - -
    Self-explanatory. - -
    Region ID for fix setforce does not exist - -
    Self-explanatory. - -
    Region ID for fix wall/region does not exist - -
    Self-explanatory. - -
    Region ID for group dynamic does not exist - -
    Self-explanatory. - -
    Region ID in variable formula does not exist - -
    Self-explanatory. - -
    Region cannot have 0 length rotation vector - -
    Self-explanatory. - -
    Region for fix oneway does not exist - -
    Self-explanatory. - -
    Region intersect region ID does not exist - -
    Self-explanatory. - -
    Region union or intersect cannot be dynamic - -
    The sub-regions can be dynamic, but not the combined region. - -
    Region union region ID does not exist - -
    One or more of the region IDs specified by the region union command -does not exist. - -
    Replacing a fix, but new style != old style - -
    A fix ID can be used a 2nd time, but only if the style matches the -previous fix. In this case it is assumed you with to reset a fix's -parameters. This error may mean you are mistakenly re-using a fix ID -when you do not intend to. - -
    Replicate command before simulation box is defined - -
    The replicate command cannot be used before a read_data, read_restart, -or create_box command. - -
    Replicate did not assign all atoms correctly - -
    Atoms replicated by the replicate command were not assigned correctly -to processors. This is likely due to some atom coordinates being -outside a non-periodic simulation box. - -
    Replicated system atom IDs are too big - -
    See the setting for tagint in the src/lmptype.h file. - -
    Replicated system is too big - -
    See the setting for bigint in the src/lmptype.h file. - -
    Required border comm not yet implemented with Kokkos - -
    There are various limitations in the communication options supported -by Kokkos. - -
    Rerun command before simulation box is defined - -
    The rerun command cannot be used before a read_data, read_restart, or -create_box command. - -
    Rerun dump file does not contain requested snapshot - -
    Self-explanatory. - -
    Resetting timestep size is not allowed with fix move - -
    This is because fix move is moving atoms based on elapsed time. - -
    Respa inner cutoffs are invalid - -
    The first cutoff must be <= the second cutoff. - -
    Respa levels must be >= 1 - -
    Self-explanatory. - -
    Respa middle cutoffs are invalid - -
    The first cutoff must be <= the second cutoff. - -
    Restart file MPI-IO output not allowed with % in filename - -
    This is because a % signifies one file per processor and MPI-IO -creates one large file for all processors. - -
    Restart file byte ordering is not recognized - -
    The file does not appear to be a LAMMPS restart file since it doesn't -contain a recognized byte-orderomg flag at the beginning. - -
    Restart file byte ordering is swapped - -
    The file was written on a machine with different byte-ordering than -the machine you are reading it on. Convert it to a text data file -instead, on the machine you wrote it on. - -
    Restart file incompatible with current version - -
    This is probably because you are trying to read a file created with a -version of LAMMPS that is too old compared to the current version. -Use your older version of LAMMPS and convert the restart file -to a data file. - -
    Restart file is a MPI-IO file - -
    The file is inconsistent with the filename you specified for it. - -
    Restart file is a multi-proc file - -
    The file is inconsistent with the filename you specified for it. - -
    Restart file is not a MPI-IO file - -
    The file is inconsistent with the filename you specified for it. - -
    Restart file is not a multi-proc file - -
    The file is inconsistent with the filename you specified for it. - -
    Restart variable returned a bad timestep - -
    The variable must return a timestep greater than the current timestep. - -
    Restrain atoms %d %d %d %d missing on proc %d at step %ld - -
    The 4 atoms in a restrain dihedral specified by the fix restrain -command are not all accessible to a processor. This probably means an -atom has moved too far. - -
    Restrain atoms %d %d %d missing on proc %d at step %ld - -
    The 3 atoms in a restrain angle specified by the fix restrain -command are not all accessible to a processor. This probably means an -atom has moved too far. - -
    Restrain atoms %d %d missing on proc %d at step %ld - -
    The 2 atoms in a restrain bond specified by the fix restrain -command are not all accessible to a processor. This probably means an -atom has moved too far. - -
    Reuse of compute ID - -
    A compute ID cannot be used twice. - -
    Reuse of dump ID - -
    A dump ID cannot be used twice. - -
    Reuse of molecule template ID - -
    The template IDs must be unique. - -
    Reuse of region ID - -
    A region ID cannot be used twice. - -
    Rigid body atoms %d %d missing on proc %d at step %ld - -
    This means that an atom cannot find the atom that owns the rigid body -it is part of, or vice versa. The solution is to use the communicate -cutoff command to insure ghost atoms are acquired from far enough away -to encompass the max distance printed when the fix rigid/small command -was invoked. - -
    Rigid body has degenerate moment of inertia - -
    Fix poems will only work with bodies (collections of atoms) that have -non-zero principal moments of inertia. This means they must be 3 or -more non-collinear atoms, even with joint atoms removed. - -
    Rigid fix must come before NPT/NPH fix - -
    NPT/NPH fix must be defined in input script after all rigid fixes, -else the rigid fix contribution to the pressure virial is -incorrect. - -
    Rmask function in equal-style variable formula - -
    Rmask is per-atom operation. - -
    Run command before simulation box is defined - -
    The run command cannot be used before a read_data, read_restart, or -create_box command. - -
    Run command start value is after start of run - -
    Self-explanatory. - -
    Run command stop value is before end of run - -
    Self-explanatory. - -
    Run_style command before simulation box is defined - -
    The run_style command cannot be used before a read_data, -read_restart, or create_box command. - -
    SRD bin size for fix srd differs from user request - -
    Fix SRD had to adjust the bin size to fit the simulation box. See the -cubic keyword if you want this message to be an error vs warning. - -
    SRD bins for fix srd are not cubic enough - -
    The bin shape is not within tolerance of cubic. See the cubic -keyword if you want this message to be an error vs warning. - -
    SRD particle %d started inside big particle %d on step %ld bounce %d - -
    See the inside keyword if you want this message to be an error vs -warning. - -
    SRD particle %d started inside wall %d on step %ld bounce %d - -
    See the inside keyword if you want this message to be an error vs -warning. - -
    Same dimension twice in fix ave/spatial - -
    Self-explanatory. - -
    Sending partition in processors part command is already a sender - -
    Cannot specify a partition to be a sender twice. - -
    Set command before simulation box is defined - -
    The set command cannot be used before a read_data, read_restart, -or create_box command. - -
    Set command floating point vector does not exist - -
    Self-explanatory. - -
    Set command integer vector does not exist - -
    Self-explanatory. - -
    Set command with no atoms existing - -
    No atoms are yet defined so the set command cannot be used. - -
    Set region ID does not exist - -
    Region ID specified in set command does not exist. - -
    Shake angles have different bond types - -
    All 3-atom angle-constrained SHAKE clusters specified by the fix shake -command that are the same angle type, must also have the same bond -types for the 2 bonds in the angle. - -
    Shake atoms %d %d %d %d missing on proc %d at step %ld - -
    The 4 atoms in a single shake cluster specified by the fix shake -command are not all accessible to a processor. This probably means -an atom has moved too far. - -
    Shake atoms %d %d %d missing on proc %d at step %ld - -
    The 3 atoms in a single shake cluster specified by the fix shake -command are not all accessible to a processor. This probably means -an atom has moved too far. - -
    Shake atoms %d %d missing on proc %d at step %ld - -
    The 2 atoms in a single shake cluster specified by the fix shake -command are not all accessible to a processor. This probably means -an atom has moved too far. - -
    Shake cluster of more than 4 atoms - -
    A single cluster specified by the fix shake command can have no more -than 4 atoms. - -
    Shake clusters are connected - -
    A single cluster specified by the fix shake command must have a single -central atom with up to 3 other atoms bonded to it. - -
    Shake determinant = 0.0 - -
    The determinant of the matrix being solved for a single cluster -specified by the fix shake command is numerically invalid. - -
    Shake fix must come before NPT/NPH fix - -
    NPT fix must be defined in input script after SHAKE fix, else the -SHAKE fix contribution to the pressure virial is incorrect. - -
    Shear history overflow, boost neigh_modify one - -
    There are too many neighbors of a single atom. Use the neigh_modify -command to increase the max number of neighbors allowed for one atom. -You may also want to boost the page size. - -
    Small to big integers are not sized correctly - -
    This error occurs whenthe sizes of smallint, imageint, tagint, bigint, -as defined in src/lmptype.h are not what is expected. Contact -the developers if this occurs. - -
    Smallint setting in lmptype.h is invalid - -
    It has to be the size of an integer. - -
    Smallint setting in lmptype.h is not compatible - -
    Smallint stored in restart file is not consistent with LAMMPS version -you are running. - -
    Special list size exceeded in fix bond/create - -
    See the read_data command for info on setting the "extra special per -atom" header value to allow for additional special values to be -stored. - -
    Specified processors != physical processors - -
    The 3d grid of processors defined by the processors command does not -match the number of processors LAMMPS is being run on. - -
    Specified target stress must be uniaxial or hydrostatic - -
    Self-explanatory. - -
    Sqrt of negative value in variable formula - -
    Self-explanatory. - -
    Substitution for illegal variable - -
    Input script line contained a variable that could not be substituted -for. - -
    Support for writing images in JPEG format not included - -
    LAMMPS was not built with the -DLAMMPS_JPEG switch in the Makefile. - -
    Support for writing images in PNG format not included - -
    LAMMPS was not built with the -DLAMMPS_PNG switch in the Makefile. - -
    Support for writing movies not included - -
    LAMMPS was not built with the -DLAMMPS_FFMPEG switch in the Makefile - -
    System in data file is too big - -
    See the setting for bigint in the src/lmptype.h file. - -
    System is not charge neutral, net charge = %g - -
    The total charge on all atoms on the system is not 0.0, which -is not valid for the long-range Coulombic solvers. - -
    TAD nsteps must be multiple of t_event - -
    Self-explanatory. - -
    TIP4P hydrogen has incorrect atom type - -
    The TIP4P pairwise computation found an H atom whose type does not -agree with the specified H type. - -
    TIP4P hydrogen is missing - -
    The TIP4P pairwise computation failed to find the correct H atom -within a water molecule. - -
    TMD target file did not list all group atoms - -
    The target file for the fix tmd command did not list all atoms in the -fix group. - -
    Tad command before simulation box is defined - -
    Self-explanatory. - -
    Tagint setting in lmptype.h is invalid - -
    Tagint must be as large or larger than smallint. - -
    Tagint setting in lmptype.h is not compatible - -
    Format of tagint stored in restart file is not consistent with LAMMPS -version you are running. See the settings in src/lmptype.h - -
    Target pressure for fix rigid/nph cannot be < 0.0 - -
    Self-explanatory. - -
    Target pressure for fix rigid/npt/small cannot be < 0.0 - -
    Self-explanatory. - -
    Target temperature for fix nvt/npt/nph cannot be 0.0 - -
    Self-explanatory. - -
    Target temperature for fix rigid/npt cannot be 0.0 - -
    Self-explanatory. - -
    Target temperature for fix rigid/npt/small cannot be 0.0 - -
    Self-explanatory. - -
    Target temperature for fix rigid/nvt cannot be 0.0 - -
    Self-explanatory. - -
    Target temperature for fix rigid/nvt/small cannot be 0.0 - -
    Self-explanatory. - -
    Temper command before simulation box is defined - -
    The temper command cannot be used before a read_data, read_restart, or -create_box command. - -
    Temperature ID for fix bond/swap does not exist - -
    Self-explanatory. - -
    Temperature ID for fix box/relax does not exist - -
    Self-explanatory. - -
    Temperature ID for fix nvt/npt does not exist - -
    Self-explanatory. - -
    Temperature ID for fix press/berendsen does not exist - -
    Self-explanatory. - -
    Temperature ID for fix rigid nvt/npt/nph does not exist - -
    Self-explanatory. - -
    Temperature ID for fix temp/berendsen does not exist - -
    Self-explanatory. - -
    Temperature ID for fix temp/csvr does not exist - -
    Self-explanatory. - -
    Temperature ID for fix temp/rescale does not exist - -
    Self-explanatory. - -
    Temperature control can not be used with fix nph - -
    Self-explanatory. - -
    Temperature control can not be used with fix nph/asphere - -
    Self-explanatory. - -
    Temperature control can not be used with fix nph/sphere - -
    Self-explanatory. - -
    Temperature control must be used with fix nphug - -
    The temp keyword must be provided. - -
    Temperature control must be used with fix npt - -
    Self-explanatory. - -
    Temperature control must be used with fix npt/asphere - -
    Self-explanatory. - -
    Temperature control must be used with fix npt/sphere - -
    Self-explanatory. - -
    Temperature control must be used with fix nvt - -
    Self-explanatory. - -
    Temperature control must be used with fix nvt/asphere - -
    Self-explanatory. - -
    Temperature control must be used with fix nvt/sllod - -
    Self-explanatory. - -
    Temperature control must be used with fix nvt/sphere - -
    Self-explanatory. - -
    Temperature control must not be used with fix nph/small - -
    Self-explanatory. - -
    Temperature for fix nvt/sllod does not have a bias - -
    The specified compute must compute temperature with a bias. - -
    Tempering could not find thermo_pe compute - -
    This compute is created by the thermo command. It must have been -explicitly deleted by a uncompute command. - -
    Tempering fix ID is not defined - -
    The fix ID specified by the temper command does not exist. - -
    Tempering temperature fix is not valid - -
    The fix specified by the temper command is not one that controls -temperature (nvt or langevin). - -
    Test_descriptor_string already allocated - -
    This is an internal error. Contact the developers. - -
    The package gpu command is required for gpu styles - -
    Self-explanatory. - -
    Thermo and fix not computed at compatible times - -
    Fixes generate values on specific timesteps. The thermo output -does not match these timesteps. - -
    Thermo compute array is accessed out-of-range - -
    Self-explanatory. - -
    Thermo compute does not compute array - -
    Self-explanatory. - -
    Thermo compute does not compute scalar - -
    Self-explanatory. - -
    Thermo compute does not compute vector - -
    Self-explanatory. - -
    Thermo compute vector is accessed out-of-range - -
    Self-explanatory. - -
    Thermo custom variable cannot be indexed - -
    Self-explanatory. - -
    Thermo custom variable is not equal-style variable - -
    Only equal-style variables can be output with thermodynamics, not -atom-style variables. - -
    Thermo every variable returned a bad timestep - -
    The variable must return a timestep greater than the current timestep. - -
    Thermo fix array is accessed out-of-range - -
    Self-explanatory. - -
    Thermo fix does not compute array - -
    Self-explanatory. - -
    Thermo fix does not compute scalar - -
    Self-explanatory. - -
    Thermo fix does not compute vector - -
    Self-explanatory. - -
    Thermo fix vector is accessed out-of-range - -
    Self-explanatory. - -
    Thermo keyword in variable requires thermo to use/init pe - -
    You are using a thermo keyword in a variable that requires -potential energy to be calculated, but your thermo output -does not use it. Add it to your thermo output. - -
    Thermo keyword in variable requires thermo to use/init press - -
    You are using a thermo keyword in a variable that requires pressure to -be calculated, but your thermo output does not use it. Add it to your -thermo output. - -
    Thermo keyword in variable requires thermo to use/init temp - -
    You are using a thermo keyword in a variable that requires temperature -to be calculated, but your thermo output does not use it. Add it to -your thermo output. - -
    Thermo style does not use press - -
    Cannot use thermo_modify to set this parameter since the thermo_style -is not computing this quantity. - -
    Thermo style does not use temp - -
    Cannot use thermo_modify to set this parameter since the thermo_style -is not computing this quantity. - -
    Thermo_modify every variable returned a bad timestep - -
    The returned timestep is less than or equal to the current timestep. - -
    Thermo_modify int format does not contain d character - -
    Self-explanatory. - -
    Thermo_modify pressure ID does not compute pressure - -
    The specified compute ID does not compute pressure. - -
    Thermo_modify temperature ID does not compute temperature - -
    The specified compute ID does not compute temperature. - -
    Thermo_style command before simulation box is defined - -
    The thermo_style command cannot be used before a read_data, -read_restart, or create_box command. - -
    This variable thermo keyword cannot be used between runs - -
    Keywords that refer to time (such as cpu, elapsed) do not -make sense in between runs. - -
    Threshhold for an atom property that isn't allocated - -
    A dump threshhold has been requested on a quantity that is -not defined by the atom style used in this simulation. - -
    Timestep must be >= 0 - -
    Specified timestep is invalid. - -
    Too big a problem to use velocity create loop all - -
    The system size must fit in a 32-bit integer to use this option. - -
    Too big a timestep - -
    Specified timestep is too large. - -
    Too big a timestep for dump dcd - -
    The timestep must fit in a 32-bit integer to use this dump style. - -
    Too big a timestep for dump xtc - -
    The timestep must fit in a 32-bit integer to use this dump style. - -
    Too few bits for lookup table - -
    Table size specified via pair_modify command does not work with your -machine's floating point representation. - -
    Too many -pk arguments in command line - -
    The string formed by concatenating the arguments is too long. Use a -package command in the input script instead. - -
    Too many MSM grid levels - -
    The max number of MSM grid levels is hardwired to 10. - -
    Too many args in variable function - -
    More args are used than any variable function allows. - -
    Too many atom pairs for pair bop - -
    The number of atomic pairs exceeds the expected number. Check your -atomic structure to ensure that it is realistic. - -
    Too many atom sorting bins - -
    This is likely due to an immense simulation box that has blown up -to a large size. - -
    Too many atom triplets for pair bop - -
    The number of three atom groups for angle determinations exceeds the -expected number. Check your atomic structrure to ensure that it is -realistic. - -
    Too many atoms for dump dcd - -
    The system size must fit in a 32-bit integer to use this dump -style. - -
    Too many atoms for dump xtc - -
    The system size must fit in a 32-bit integer to use this dump -style. - -
    Too many atoms to dump sort - -
    Cannot sort when running with more than 2^31 atoms. - -
    Too many exponent bits for lookup table - -
    Table size specified via pair_modify command does not work with your -machine's floating point representation. - -
    Too many groups - -
    The maximum number of atom groups (including the "all" group) is -given by MAX_GROUP in group.cpp and is 32. - -
    Too many iterations - -
    You must use a number of iterations that fit in a 32-bit integer -for minimization. - -
    Too many lines in one body in data file - boost MAXBODY - -
    MAXBODY is a setting at the top of the src/read_data.cpp file. -Set it larger and re-compile the code. - -
    Too many local+ghost atoms for neighbor list - -
    The number of nlocal + nghost atoms on a processor -is limited by the size of a 32-bit integer with 2 bits -removed for masking 1-2, 1-3, 1-4 neighbors. - -
    Too many mantissa bits for lookup table - -
    Table size specified via pair_modify command does not work with your -machine's floating point representation. - -
    Too many masses for fix shake - -
    The fix shake command cannot list more masses than there are atom -types. - -
    Too many molecules for fix poems - -
    The limit is 2^31 = ~2 billion molecules. - -
    Too many molecules for fix rigid - -
    The limit is 2^31 = ~2 billion molecules. - -
    Too many neighbor bins - -
    This is likely due to an immense simulation box that has blown up -to a large size. - -
    Too many timesteps - -
    The cummulative timesteps must fit in a 64-bit integer. - -
    Too many timesteps for NEB - -
    You must use a number of timesteps that fit in a 32-bit integer -for NEB. - -
    Too many total atoms - -
    See the setting for bigint in the src/lmptype.h file. - -
    Too many total bits for bitmapped lookup table - -
    Table size specified via pair_modify command is too large. Note that -a value of N generates a 2^N size table. - -
    Too much buffered per-proc info for dump - -
    The size of the buffered string must fit in a 32-bit integer for a -dump. - -
    Too much per-proc info for dump - -
    Number of local atoms times number of columns must fit in a 32-bit -integer for dump. - -
    Tree structure in joint connections - -
    Fix poems cannot (yet) work with coupled bodies whose joints connect -the bodies in a tree structure. - -
    Triclinic box skew is too large - -
    The displacement in a skewed direction must be less than half the box -length in that dimension. E.g. the xy tilt must be between -half and -+half of the x box length. This constraint can be relaxed by using -the box tilt command. - -
    Tried to convert a double to int, but input_double > INT_MAX - -
    Self-explanatory. - -
    Trying to build an occasional neighbor list before initialization completed - -
    This is not allowed. Source code caller needs to be modified. - -
    Two fix ave commands using same compute chunk/atom command in incompatible ways - -
    They are both attempting to "lock" the chunk/atom command so that the -chunk assignments persist for some number of timesteps, but are doing -it in different ways. - -
    Two groups cannot be the same in fix spring couple - -
    Self-explanatory. - -
    USER-CUDA mode requires CUDA variant of min style - -
    CUDA mode is enabled, so the min style must include a cuda suffix. - -
    USER-CUDA mode requires CUDA variant of run style - -
    CUDA mode is enabled, so the run style must include a cuda suffix. - -
    USER-CUDA package does not yet support comm_style tiled - -
    Self-explanatory. - -
    USER-CUDA package requires a cuda enabled atom_style - -
    Self-explanatory. - -
    Unable to initialize accelerator for use - -
    There was a problem initializing an accelerator for the gpu package - -
    Unbalanced quotes in input line - -
    No matching end double quote was found following a leading double -quote. - -
    Unexpected end of -reorder file - -
    Self-explanatory. - -
    Unexpected end of AngleCoeffs section - -
    Read a blank line. - -
    Unexpected end of BondCoeffs section - -
    Read a blank line. - -
    Unexpected end of DihedralCoeffs section - -
    Read a blank line. - -
    Unexpected end of ImproperCoeffs section - -
    Read a blank line. - -
    Unexpected end of PairCoeffs section - -
    Read a blank line. - -
    Unexpected end of custom file - -
    Self-explanatory. - -
    Unexpected end of data file - -
    LAMMPS hit the end of the data file while attempting to read a -section. Something is wrong with the format of the data file. - -
    Unexpected end of dump file - -
    A read operation from the file failed. - -
    Unexpected end of fix rigid file - -
    A read operation from the file failed. - -
    Unexpected end of fix rigid/small file - -
    A read operation from the file failed. - -
    Unexpected end of molecule file - -
    Self-explanatory. - -
    Unexpected end of neb file - -
    A read operation from the file failed. - -
    Units command after simulation box is defined - -
    The units command cannot be used after a read_data, read_restart, or -create_box command. - -
    Universe/uloop variable count < # of partitions - -
    A universe or uloop style variable must specify a number of values >= to the -number of processor partitions. - -
    Unknown angle style - -
    The choice of angle style is unknown. - -
    Unknown atom style - -
    The choice of atom style is unknown. - -
    Unknown body style - -
    The choice of body style is unknown. - -
    Unknown bond style - -
    The choice of bond style is unknown. - -
    Unknown command: %s - -
    The command is not known to LAMMPS. Check the input script. - -
    Unknown compute style - -
    The choice of compute style is unknown. - -
    Unknown dihedral style - -
    The choice of dihedral style is unknown. - -
    Unknown dump reader style - -
    The choice of dump reader style via the format keyword is unknown. - -
    Unknown dump style - -
    The choice of dump style is unknown. - -
    Unknown error in GPU library - -
    Self-explanatory. - -
    Unknown fix style - -
    The choice of fix style is unknown. - -
    Unknown identifier in data file: %s - -
    A section of the data file cannot be read by LAMMPS. - -
    Unknown improper style - -
    The choice of improper style is unknown. - -
    Unknown keyword in thermo_style custom command - -
    One or more specified keywords are not recognized. - -
    Unknown kspace style - -
    The choice of kspace style is unknown. - -
    Unknown pair style - -
    The choice of pair style is unknown. - -
    Unknown pair_modify hybrid sub-style - -
    The choice of sub-style is unknown. - -
    Unknown region style - -
    The choice of region style is unknown. - -
    Unknown section in molecule file - -
    Self-explanatory. - -
    Unknown table style in angle style table - -
    Self-explanatory. - -
    Unknown table style in bond style table - -
    Self-explanatory. - -
    Unknown table style in pair_style command - -
    Style of table is invalid for use with pair_style table command. - -
    Unknown unit_style - -
    Self-explanatory. Check the input script or data file. - -
    Unrecognized lattice type in MEAM file 1 - -
    The lattice type in an entry of the MEAM library file is not -valid. - -
    Unrecognized lattice type in MEAM file 2 - -
    The lattice type in an entry of the MEAM parameter file is not -valid. - -
    Unrecognized pair style in compute pair command - -
    Self-explanatory. - -
    Unrecognized virial argument in pair_style command - -
    Only two options are supported: LAMMPSvirial and KIMvirial - -
    Unsupported mixing rule in kspace_style ewald/disp - -
    Only geometric mixing is supported. - -
    Unsupported order in kspace_style ewald/disp - -
    Only 1/r^6 dispersion or dipole terms are supported. - -
    Unsupported order in kspace_style pppm/disp, pair_style %s - -
    Only pair styles with 1/r and 1/r^6 dependence are currently supported. - -
    Using fix nvt/sllod with inconsistent fix deform remap option - -
    Fix nvt/sllod requires that deforming atoms have a velocity profile -provided by "remap v" as a fix deform option. - -
    Using fix nvt/sllod with no fix deform defined - -
    Self-explanatory. - -
    Using fix srd with inconsistent fix deform remap option - -
    When shearing the box in an SRD simulation, the remap v option for fix -deform needs to be used. - -
    Using pair lubricate with inconsistent fix deform remap option - -
    Must use remap v option with fix deform with this pair style. - -
    Using pair lubricate/poly with inconsistent fix deform remap option - -
    If fix deform is used, the remap v option is required. - -
    Using suffix cuda without USER-CUDA package enabled - -
    Self-explanatory. - -
    Using suffix gpu without GPU package installed - -
    Self-explanatory. - -
    Using suffix intel without USER-INTEL package installed - -
    Self-explanatory. - -
    Using suffix kk without KOKKOS package enabled - -
    Self-explanatory. - -
    Using suffix omp without USER-OMP package installed - -
    Self-explanatory. - -
    Variable ID in variable formula does not exist - -
    Self-explanatory. - -
    Variable atom ID is too large - -
    Specified ID is larger than the maximum allowed atom ID. - -
    Variable evaluation before simulation box is defined - -
    Cannot evaluate a compute or fix or atom-based value in a variable -before the simulation has been setup. - -
    Variable evaluation in fix wall gave bad value - -
    The returned value for epsilon or sigma < 0.0. - -
    Variable evaluation in region gave bad value - -
    Variable returned a radius < 0.0. - -
    Variable for compute ti is invalid style - -
    Self-explanatory. - -
    Variable for create_atoms is invalid style - -
    The variables must be equal-style variables. - -
    Variable for dump every is invalid style - -
    Only equal-style variables can be used. - -
    Variable for dump image center is invalid style - -
    Must be an equal-style variable. - -
    Variable for dump image persp is invalid style - -
    Must be an equal-style variable. - -
    Variable for dump image phi is invalid style - -
    Must be an equal-style variable. - -
    Variable for dump image theta is invalid style - -
    Must be an equal-style variable. - -
    Variable for dump image zoom is invalid style - -
    Must be an equal-style variable. - -
    Variable for fix adapt is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix addforce is invalid style - -
    Self-explanatory. - -
    Variable for fix aveforce is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix deform is invalid style - -
    The variable must be an equal-style variable. - -
    Variable for fix efield is invalid style - -
    The variable must be an equal- or atom-style variable. - -
    Variable for fix gravity is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix heat is invalid style - -
    Only equal-style or atom-style variables can be used. - -
    Variable for fix indent is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix indent is not equal style - -
    Only equal-style variables can be used. - -
    Variable for fix langevin is invalid style - -
    It must be an equal-style variable. - -
    Variable for fix move is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix setforce is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix temp/berendsen is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix temp/csvr is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix temp/rescale is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix wall is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix wall/reflect is invalid style - -
    Only equal-style variables can be used. - -
    Variable for fix wall/srd is invalid style - -
    Only equal-style variables can be used. - -
    Variable for group dynamic is invalid style - -
    The variable must be an atom-style variable. - -
    Variable for group is invalid style - -
    Only atom-style variables can be used. - -
    Variable for region cylinder is invalid style - -
    Only equal-style varaibles are allowed. - -
    Variable for region is invalid style - -
    Only equal-style variables can be used. - -
    Variable for region is not equal style - -
    Self-explanatory. - -
    Variable for region sphere is invalid style - -
    Only equal-style varaibles are allowed. - -
    Variable for restart is invalid style - -
    Only equal-style variables can be used. - -
    Variable for set command is invalid style - -
    Only atom-style variables can be used. - -
    Variable for thermo every is invalid style - -
    Only equal-style variables can be used. - -
    Variable for velocity set is invalid style - -
    Only atom-style variables can be used. - -
    Variable for voronoi radius is not atom style - -
    Self-explanatory. - -
    Variable formula compute array is accessed out-of-range - -
    Self-explanatory. - -
    Variable formula compute vector is accessed out-of-range - -
    Self-explanatory. - -
    Variable formula fix array is accessed out-of-range - -
    Self-explanatory. - -
    Variable formula fix vector is accessed out-of-range - -
    Self-explanatory. - -
    Variable has circular dependency - -
    A circular dependency is when variable "a" in used by variable "b" and -variable "b" is also used by varaible "a". Circular dependencies with -longer chains of dependence are also not allowed. - -
    Variable name between brackets must be alphanumeric or underscore characters - -
    Self-explanatory. - -
    Variable name for compute chunk/atom does not exist - -
    Self-explanatory. - -
    Variable name for compute reduce does not exist - -
    Self-explanatory. - -
    Variable name for compute ti does not exist - -
    Self-explanatory. - -
    Variable name for create_atoms does not exist - -
    Self-explanatory. - -
    Variable name for dump every does not exist - -
    Self-explanatory. - -
    Variable name for dump image center does not exist - -
    Self-explanatory. - -
    Variable name for dump image persp does not exist - -
    Self-explanatory. - -
    Variable name for dump image phi does not exist - -
    Self-explanatory. - -
    Variable name for dump image theta does not exist - -
    Self-explanatory. - -
    Variable name for dump image zoom does not exist - -
    Self-explanatory. - -
    Variable name for fix adapt does not exist - -
    Self-explanatory. - -
    Variable name for fix addforce does not exist - -
    Self-explanatory. - -
    Variable name for fix ave/atom does not exist - -
    Self-explanatory. - -
    Variable name for fix ave/chunk does not exist - -
    Self-explanatory. - -
    Variable name for fix ave/correlate does not exist - -
    Self-explanatory. - -
    Variable name for fix ave/histo does not exist - -
    Self-explanatory. - -
    Variable name for fix ave/spatial does not exist - -
    Self-explanatory. - -
    Variable name for fix ave/time does not exist - -
    Self-explanatory. - -
    Variable name for fix aveforce does not exist - -
    Self-explanatory. - -
    Variable name for fix deform does not exist - -
    Self-explantory. - -
    Variable name for fix efield does not exist - -
    Self-explanatory. - -
    Variable name for fix gravity does not exist - -
    Self-explanatory. - -
    Variable name for fix heat does not exist - -
    Self-explanatory. - -
    Variable name for fix indent does not exist - -
    Self-explanatory. - -
    Variable name for fix langevin does not exist - -
    Self-explanatory. - -
    Variable name for fix move does not exist - -
    Self-explanatory. - -
    Variable name for fix setforce does not exist - -
    Self-explanatory. - -
    Variable name for fix store/state does not exist - -
    Self-explanatory. - -
    Variable name for fix temp/berendsen does not exist - -
    Self-explanatory. - -
    Variable name for fix temp/csvr does not exist - -
    Self-explanatory. - -
    Variable name for fix temp/rescale does not exist - -
    Self-explanatory. - -
    Variable name for fix vector does not exist - -
    Self-explanatory. - -
    Variable name for fix wall does not exist - -
    Self-explanatory. - -
    Variable name for fix wall/reflect does not exist - -
    Self-explanatory. - -
    Variable name for fix wall/srd does not exist - -
    Self-explanatory. - -
    Variable name for group does not exist - -
    Self-explanatory. - -
    Variable name for group dynamic does not exist - -
    Self-explanatory. - -
    Variable name for region cylinder does not exist - -
    Self-explanatory. - -
    Variable name for region does not exist - -
    Self-explanatory. - -
    Variable name for region sphere does not exist - -
    Self-explanatory. - -
    Variable name for restart does not exist - -
    Self-explanatory. - -
    Variable name for set command does not exist - -
    Self-explanatory. - -
    Variable name for thermo every does not exist - -
    Self-explanatory. - -
    Variable name for velocity set does not exist - -
    Self-explanatory. - -
    Variable name for voronoi radius does not exist - -
    Self-explanatory. - -
    Variable name must be alphanumeric or underscore characters - -
    Self-explanatory. - -
    Variable uses atom property that isn't allocated - -
    Self-explanatory. - -
    Velocity command before simulation box is defined - -
    The velocity command cannot be used before a read_data, read_restart, -or create_box command. - -
    Velocity command with no atoms existing - -
    A velocity command has been used, but no atoms yet exist. - -
    Velocity ramp in z for a 2d problem - -
    Self-explanatory. - -
    Velocity rigid used with non-rigid fix-ID - -
    Self-explanatory. - -
    Velocity temperature ID does calculate a velocity bias - -
    The specified compute must compute a bias for temperature. - -
    Velocity temperature ID does not compute temperature - -
    The compute ID given to the velocity command must compute -temperature. - -
    Verlet/split can only currently be used with comm_style brick - -
    This is a current restriction in LAMMPS. - -
    Verlet/split does not yet support TIP4P - -
    This is a current limitation. - -
    Verlet/split requires 2 partitions - -
    See the -partition command-line switch. - -
    Verlet/split requires Rspace partition layout be multiple of Kspace partition layout in each dim - -
    This is controlled by the processors command. - -
    Verlet/split requires Rspace partition size be multiple of Kspace partition size - -
    This is so there is an equal number of Rspace processors for every -Kspace processor. - -
    Virial was not tallied on needed timestep - -
    You are using a thermo keyword that requires potentials to -have tallied the virial, but they didn't on this timestep. See the -variable doc page for ideas on how to make this work. - -
    Voro++ error: narea and neigh have a different size - -
    This error is returned by the Voro++ library. - -
    Wall defined twice in fix wall command - -
    Self-explanatory. - -
    Wall defined twice in fix wall/reflect command - -
    Self-explanatory. - -
    Wall defined twice in fix wall/srd command - -
    Self-explanatory. - -
    Water H epsilon must be 0.0 for pair style lj/cut/tip4p/cut - -
    This is because LAMMPS does not compute the Lennard-Jones interactions -with these particles for efficiency reasons. - -
    Water H epsilon must be 0.0 for pair style lj/cut/tip4p/long - -
    This is because LAMMPS does not compute the Lennard-Jones interactions -with these particles for efficiency reasons. - -
    Water H epsilon must be 0.0 for pair style lj/long/tip4p/long - -
    This is because LAMMPS does not compute the Lennard-Jones interactions -with these particles for efficiency reasons. - -
    World variable count doesn't match # of partitions - -
    A world-style variable must specify a number of values equal to the -number of processor partitions. - -
    Write_data command before simulation box is defined - -
    Self-explanatory. - -
    Write_restart command before simulation box is defined - -
    The write_restart command cannot be used before a read_data, -read_restart, or create_box command. - -
    Writing to MPI-IO filename when MPIIO package is not installed - -
    Self-explanatory. - -
    Zero length rotation vector with displace_atoms - -
    Self-explanatory. - -
    Zero length rotation vector with fix move - -
    Self-explanatory. - -
    Zero-length lattice orient vector - -
    Self-explanatory. - - -
    -

    Warnings: -

    -
    - -
    Adjusting Coulombic cutoff for MSM, new cutoff = %g - -
    The adjust/cutoff command is turned on and the Coulombic cutoff has been -adjusted to match the user-specified accuracy. - -
    Angle atoms missing at step %ld - -
    One or more of 3 atoms needed to compute a particular angle are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the angle has blown apart and an atom is -too far away. - -
    Angle style in data file differs from currently defined angle style - -
    Self-explanatory. - -
    Atom style in data file differs from currently defined atom style - -
    Self-explanatory. - -
    Bond atom missing in box size check - -
    The 2nd atoms needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. - -
    Bond atom missing in image check - -
    The 2nd atom in a particular bond is missing on this processor. -Typically this is because the pairwise cutoff is set too short or the -bond has blown apart and an atom is too far away. - -
    Bond atoms missing at step %ld - -
    The 2nd atom needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. - -
    Bond style in data file differs from currently defined bond style - -
    Self-explanatory. - -
    Bond/angle/dihedral extent > half of periodic box length - -
    This is a restriction because LAMMPS can be confused about which image -of an atom in the bonded interaction is the correct one to use. -"Extent" in this context means the maximum end-to-end length of the -bond/angle/dihedral. LAMMPS computes this by taking the maximum bond -length, multiplying by the number of bonds in the interaction (e.g. 3 -for a dihedral) and adding a small amount of stretch. - -
    Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero - -
    Self-explantory. - -
    Cannot count rigid body degrees-of-freedom before bodies are fully initialized - -
    This means the temperature associated with the rigid bodies may be -incorrect on this timestep. - -
    Cannot count rigid body degrees-of-freedom before bodies are initialized - -
    This means the temperature associated with the rigid bodies may be -incorrect on this timestep. - -
    Cannot include log terms without 1/r terms; setting flagHI to 1 - -
    Self-explanatory. - -
    Cannot include log terms without 1/r terms; setting flagHI to 1. - -
    Self-explanatory. - -
    Charges are set, but coulombic solver is not used - -
    Self-explanatory. - -
    Charges did not converge at step %ld: %lg - -
    Self-explanatory. - -
    Communication cutoff is too small for SNAP micro load balancing, increased to %lf - -
    Self-explanatory. - -
    Compute cna/atom cutoff may be too large to find ghost atom neighbors - -
    The neighbor cutoff used may not encompass enough ghost atoms -to perform this operation correctly. - -
    Computing temperature of portions of rigid bodies - -
    The group defined by the temperature compute does not encompass all -the atoms in one or more rigid bodies, so the change in -degrees-of-freedom for the atoms in those partial rigid bodies will -not be accounted for. - -
    Create_bonds max distance > minimum neighbor cutoff - -
    This means atom pairs for some atom types may not be in the neighbor -list and thus no bond can be created between them. - -
    Delete_atoms cutoff > minimum neighbor cutoff - -
    This means atom pairs for some atom types may not be in the neighbor -list and thus an atom in that pair cannot be deleted. - -
    Dihedral atoms missing at step %ld - -
    One or more of 4 atoms needed to compute a particular dihedral are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the dihedral has blown apart and an atom is -too far away. - -
    Dihedral problem - -
    Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. - -
    Dihedral problem: %d %ld %d %d %d %d - -
    Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. - -
    Dihedral style in data file differs from currently defined dihedral style - -
    Self-explanatory. - -
    Dump dcd/xtc timestamp may be wrong with fix dt/reset - -
    If the fix changes the timestep, the dump dcd file will not -reflect the change. - -
    Estimated error in splitting of dispersion coeffs is %g - -
    Error is greater than 0.0001 percent. - -
    Ewald/disp Newton solver failed, using old method to estimate g_ewald - -
    Self-explanatory. Choosing a different cutoff value may help. - -
    FENE bond too long - -
    A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. - -
    FENE bond too long: %ld %d %d %g - -
    A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. - -
    FENE bond too long: %ld %g - -
    A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. - -
    Fix SRD walls overlap but fix srd overlap not set - -
    You likely want to set this in your input script. - -
    Fix bond/swap will ignore defined angles - -
    See the doc page for fix bond/swap for more info on this -restriction. - -
    Fix evaporate may delete atom with non-zero molecule ID - -
    This is probably an error, since you should not delete only one atom -of a molecule. - -
    Fix gcmc using full_energy option - -
    Fix gcmc has automatically turned on the full_energy option since it -is required for systems like the one specified by the user. User input -included one or more of the following: kspace, triclinic, a hybrid -pair style, an eam pair style, or no "single" function for the pair -style. - -
    Fix move does not update angular momentum - -
    Atoms store this quantity, but fix move does not (yet) update it. - -
    Fix move does not update quaternions - -
    Atoms store this quantity, but fix move does not (yet) update it. - -
    Fix qeq CG convergence failed (%g) after %d iterations at %ld step - -
    Self-explanatory. - -
    Fix qeq has non-zero lower Taper radius cutoff - -
    Absolute value must be <= 0.01. - -
    Fix qeq has very low Taper radius cutoff - -
    Value should typically be >= 5.0. - -
    Fix qeq/dynamic tolerance may be too small for damped dynamics - -
    Self-explanatory. - -
    Fix rattle should come after all other integration fixes - -
    This fix is designed to work after all other integration fixes change -atom positions. Thus it should be the last integration fix specified. -If not, it will not satisfy the desired constraints as well as it -otherwise would. - -
    Fix recenter should come after all other integration fixes - -
    Other fixes may change the position of the center-of-mass, so -fix recenter should come last. - -
    Fix srd SRD moves may trigger frequent reneighboring - -
    This is because the SRD particles may move long distances. - -
    Fix srd grid size > 1/4 of big particle diameter - -
    This may cause accuracy problems. - -
    Fix srd particle moved outside valid domain - -
    This may indicate a problem with your simulation parameters. - -
    Fix srd particles may move > big particle diameter - -
    This may cause accuracy problems. - -
    Fix srd viscosity < 0.0 due to low SRD density - -
    This may cause accuracy problems. - -
    Fix thermal/conductivity comes before fix ave/spatial - -
    The order of these 2 fixes in your input script is such that fix -thermal/conductivity comes first. If you are using fix ave/spatial to -measure the temperature profile induced by fix viscosity, then this -may cause a glitch in the profile since you are averaging immediately -after swaps have occurred. Flipping the order of the 2 fixes -typically helps. - -
    Fix viscosity comes before fix ave/spatial - -
    The order of these 2 fixes in your input script is such that -fix viscosity comes first. If you are using fix ave/spatial -to measure the velocity profile induced by fix viscosity, then -this may cause a glitch in the profile since you are averaging -immediately after swaps have occurred. Flipping the order -of the 2 fixes typically helps. - -
    Fixes cannot send data in Kokkos communication, switching to classic communication - -
    This is current restriction with Kokkos. - -
    For better accuracy use 'pair_modify table 0' - -
    The user-specified force accuracy cannot be achieved unless the table -feature is disabled by using 'pair_modify table 0'. - -
    Geometric mixing assumed for 1/r^6 coefficients - -
    Self-explanatory. - -
    Group for fix_modify temp != fix group - -
    The fix_modify command is specifying a temperature computation that -computes a temperature on a different group of atoms than the fix -itself operates on. This is probably not what you want to do. - -
    H matrix size has been exceeded: m_fill=%d H.m=%d\\n - -
    This is the size of the matrix. - -
    Improper atoms missing at step %ld - -
    One or more of 4 atoms needed to compute a particular improper are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the improper has blown apart and an atom is -too far away. - -
    Improper problem: %d %ld %d %d %d %d - -
    Conformation of the 4 listed improper atoms is extreme; you may want -to check your simulation geometry. - -
    Improper style in data file differs from currently defined improper style - -
    Self-explanatory. - -
    Inconsistent image flags - -
    The image flags for a pair on bonded atoms appear to be inconsistent. -Inconsistent means that when the coordinates of the two atoms are -unwrapped using the image flags, the two atoms are far apart. -Specifically they are further apart than half a periodic box length. -Or they are more than a box length apart in a non-periodic dimension. -This is usually due to the initial data file not having correct image -flags for the 2 atoms in a bond that straddles a periodic boundary. -They should be different by 1 in that case. This is a warning because -inconsistent image flags will not cause problems for dynamics or most -LAMMPS simulations. However they can cause problems when such atoms -are used with the fix rigid or replicate commands. - -
    KIM Model does not provide `energy'; Potential energy will be zero - -
    Self-explanatory. - -
    KIM Model does not provide `forces'; Forces will be zero - -
    Self-explanatory. - -
    KIM Model does not provide `particleEnergy'; energy per atom will be zero - -
    Self-explanatory. - -
    KIM Model does not provide `particleVirial'; virial per atom will be zero - -
    Self-explanatory. - -
    Kspace_modify slab param < 2.0 may cause unphysical behavior - -
    The kspace_modify slab parameter should be larger to insure periodic -grids padded with empty space do not overlap. - -
    Less insertions than requested - -
    The fix pour command was unsuccessful at finding open space -for as many particles as it tried to insert. - -
    Library error in lammps_gather_atoms - -
    This library function cannot be used if atom IDs are not defined -or are not consecutively numbered. - -
    Library error in lammps_scatter_atoms - -
    This library function cannot be used if atom IDs are not defined or -are not consecutively numbered, or if no atom map is defined. See the -atom_modify command for details about atom maps. - -
    Lost atoms via change_box: original %ld current %ld - -
    The command options you have used caused atoms to be lost. - -
    Lost atoms via displace_atoms: original %ld current %ld - -
    The command options you have used caused atoms to be lost. - -
    Lost atoms: original %ld current %ld - -
    Lost atoms are checked for each time thermo output is done. See the -thermo_modify lost command for options. Lost atoms usually indicate -bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before -reneighboring. - -
    MSM mesh too small, increasing to 2 points in each direction - -
    Self-explanatory. - -
    Mismatch between velocity and compute groups - -
    The temperature computation used by the velocity command will not be -on the same group of atoms that velocities are being set for. - -
    Mixing forced for lj coefficients - -
    Self-explanatory. - -
    Molecule attributes do not match system attributes - -
    An attribute is specified (e.g. diameter, charge) that is -not defined for the specified atom style. - -
    Molecule has bond topology but no special bond settings - -
    This means the bonded atoms will not be excluded in pair-wise -interactions. - -
    Molecule template for create_atoms has multiple molecules - -
    The create_atoms command will only create molecules of a single type, -i.e. the first molecule in the template. - -
    Molecule template for fix gcmc has multiple molecules - -
    The fix gcmc command will only create molecules of a single type, -i.e. the first molecule in the template. - -
    Molecule template for fix shake has multiple molecules - -
    The fix shake command will only recoginze molecules of a single -type, i.e. the first molecule in the template. - -
    More than one compute centro/atom - -
    It is not efficient to use compute centro/atom more than once. - -
    More than one compute cluster/atom - -
    It is not efficient to use compute cluster/atom more than once. - -
    More than one compute cna/atom defined - -
    It is not efficient to use compute cna/atom more than once. - -
    More than one compute contact/atom - -
    It is not efficient to use compute contact/atom more than once. - -
    More than one compute coord/atom - -
    It is not efficient to use compute coord/atom more than once. - -
    More than one compute damage/atom - -
    It is not efficient to use compute ke/atom more than once. - -
    More than one compute dilatation/atom - -
    Self-explanatory. - -
    More than one compute erotate/sphere/atom - -
    It is not efficient to use compute erorate/sphere/atom more than once. - -
    More than one compute ke/atom - -
    It is not efficient to use compute ke/atom more than once. - -
    More than one compute plasticity/atom - -
    Self-explanatory. - -
    More than one compute sna/atom - -
    Self-explanatory. - -
    More than one compute snad/atom - -
    Self-explanatory. - -
    More than one compute snav/atom - -
    Self-explanatory. - -
    More than one fix poems - -
    It is not efficient to use fix poems more than once. - -
    More than one fix rigid - -
    It is not efficient to use fix rigid more than once. - -
    Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies - -
    This is because excluding specific pair interactions also excludes -them from long-range interactions which may not be the desired effect. -The special_bonds command handles this consistently by insuring -excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated -consistently by both the short-range pair style and the long-range -solver. This is not done for exclusions of charged atom pairs via the -neigh_modify exclude command. - -
    New thermo_style command, previous thermo_modify settings will be lost - -
    If a thermo_style command is used after a thermo_modify command, the -settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify commmand acts on -the currently defined thermo style, and a thermo_style command creates -a new style. - -
    No Kspace calculation with verlet/split - -
    The 2nd partition performs a kspace calculation so the kspace_style -command must be used. - -
    No automatic unit conversion to XTC file format conventions possible for units lj - -
    This means no scaling will be performed. - -
    No fixes defined, atoms won't move - -
    If you are not using a fix like nve, nvt, npt then atom velocities and -coordinates will not be updated during timestepping. - -
    No joints between rigid bodies, use fix rigid instead - -
    The bodies defined by fix poems are not connected by joints. POEMS -will integrate the body motion, but it would be more efficient to use -fix rigid. - -
    Not using real units with pair reax - -
    This is most likely an error, unless you have created your own ReaxFF -parameter file in a different set of units. - -
    Number of MSM mesh points changed to be a multiple of 2 - -
    MSM requires that the number of grid points in each direction be a multiple -of two and the number of grid points in one or more directions have been -adjusted to meet this requirement. - -
    OMP_NUM_THREADS environment is not set. - -
    This environment variable must be set appropriately to use the -USER-OMP pacakge. - -
    One or more atoms are time integrated more than once - -
    This is probably an error since you typically do not want to -advance the positions or velocities of an atom more than once -per timestep. - -
    One or more chunks do not contain all atoms in molecule - -
    This may not be what you intended. - -
    One or more dynamic groups may not be updated at correct point in timestep - -
    If there are other fixes that act immediately after the intitial stage -of time integration within a timestep (i.e. after atoms move), then -the command that sets up the dynamic group should appear after those -fixes. This will insure that dynamic group assignements are made -after all atoms have moved. - -
    One or more respa levels compute no forces - -
    This is computationally inefficient. - -
    Pair COMB charge %.10f with force %.10f hit max barrier - -
    Something is possibly wrong with your model. - -
    Pair COMB charge %.10f with force %.10f hit min barrier - -
    Something is possibly wrong with your model. - -
    Pair brownian needs newton pair on for momentum conservation - -
    Self-explanatory. - -
    Pair dpd needs newton pair on for momentum conservation - -
    Self-explanatory. - -
    Pair dsmc: num_of_collisions > number_of_A - -
    Collision model in DSMC is breaking down. - -
    Pair dsmc: num_of_collisions > number_of_B - -
    Collision model in DSMC is breaking down. - -
    Pair style in data file differs from currently defined pair style - -
    Self-explanatory. - -
    Particle deposition was unsuccessful - -
    The fix deposit command was not able to insert as many atoms as -needed. The requested volume fraction may be too high, or other atoms -may be in the insertion region. - -
    Proc sub-domain size < neighbor skin, could lead to lost atoms - -
    The decomposition of the physical domain (likely due to load -balancing) has led to a processor's sub-domain being smaller than the -neighbor skin in one or more dimensions. Since reneighboring is -triggered by atoms moving the skin distance, this may lead to lost -atoms, if an atom moves all the way across a neighboring processor's -sub-domain before reneighboring is triggered. - -
    Reducing PPPM order b/c stencil extends beyond nearest neighbor processor - -
    This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. - -
    Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor - -
    This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. - -
    Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor - -
    This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. - -
    Replacing a fix, but new group != old group - -
    The ID and style of a fix match for a fix you are changing with a fix -command, but the new group you are specifying does not match the old -group. - -
    Replicating in a non-periodic dimension - -
    The parameters for a replicate command will cause a non-periodic -dimension to be replicated; this may cause unwanted behavior. - -
    Resetting reneighboring criteria during PRD - -
    A PRD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. - -
    Resetting reneighboring criteria during TAD - -
    A TAD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. - -
    Resetting reneighboring criteria during minimization - -
    Minimization requires that neigh_modify settings be delay = 0, every = -1, check = yes. Since these settings were not in place, LAMMPS -changed them and will restore them to their original values after the -minimization. - -
    Restart file used different # of processors - -
    The restart file was written out by a LAMMPS simulation running on a -different number of processors. Due to round-off, the trajectories of -your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. - -
    Restart file used different 3d processor grid - -
    The restart file was written out by a LAMMPS simulation running on a -different 3d grid of processors. Due to round-off, the trajectories -of your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. - -
    Restart file used different boundary settings, using restart file values - -
    Your input script cannot change these restart file settings. - -
    Restart file used different newton bond setting, using restart file value - -
    The restart file value will override the setting in the input script. - -
    Restart file used different newton pair setting, using input script value - -
    The input script value will override the setting in the restart file. - -
    Restrain problem: %d %ld %d %d %d %d - -
    Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. - -
    Running PRD with only one replica - -
    This is allowed, but you will get no parallel speed-up. - -
    SRD bin shifting turned on due to small lamda - -
    This is done to try to preserve accuracy. - -
    SRD bin size for fix srd differs from user request - -
    Fix SRD had to adjust the bin size to fit the simulation box. See the -cubic keyword if you want this message to be an error vs warning. - -
    SRD bins for fix srd are not cubic enough - -
    The bin shape is not within tolerance of cubic. See the cubic -keyword if you want this message to be an error vs warning. - -
    SRD particle %d started inside big particle %d on step %ld bounce %d - -
    See the inside keyword if you want this message to be an error vs -warning. - -
    SRD particle %d started inside wall %d on step %ld bounce %d - -
    See the inside keyword if you want this message to be an error vs -warning. - -
    Shake determinant < 0.0 - -
    The determinant of the quadratic equation being solved for a single -cluster specified by the fix shake command is numerically suspect. LAMMPS -will set it to 0.0 and continue. - -
    Should not allow rigid bodies to bounce off relecting walls - -
    LAMMPS allows this, but their dynamics are not computed correctly. - -
    Should not use fix nve/limit with fix shake - -
    This will lead to invalid constraint forces in the SHAKE computation. - -
    Simulations might be very slow because of large number of structure factors - -
    Self-explanatory. - -
    Slab correction not needed for MSM - -
    Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. - -
    System is not charge neutral, net charge = %g - -
    The total charge on all atoms on the system is not 0.0, which -is not valid for the long-range Coulombic solvers. - -
    Table inner cutoff >= outer cutoff - -
    You specified an inner cutoff for a Coulombic table that is longer -than the global cutoff. Probably not what you wanted. - -
    Temperature for MSST is not for group all - -
    User-assigned temperature to MSST fix does not compute temperature for -all atoms. Since MSST computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by MSST could be inaccurate. - -
    Temperature for NPT is not for group all - -
    User-assigned temperature to NPT fix does not compute temperature for -all atoms. Since NPT computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by NPT could be inaccurate. - -
    Temperature for fix modify is not for group all - -
    The temperature compute is being used with a pressure calculation -which does operate on group all, so this may be inconsistent. - -
    Temperature for thermo pressure is not for group all - -
    User-assigned temperature to thermo via the thermo_modify command does -not compute temperature for all atoms. Since thermo computes a global -pressure, the kinetic energy contribution from the temperature is -assumed to also be for all atoms. Thus the pressure printed by thermo -could be inaccurate. - -
    The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015 - -
    Self-explanatory. - -
    The minimizer does not re-orient dipoles when using fix efield - -
    This means that only the atom coordinates will be minimized, -not the orientation of the dipoles. - -
    Too many common neighbors in CNA %d times - -
    More than the maximum # of neighbors was found multiple times. This -was unexpected. - -
    Too many inner timesteps in fix ttm - -
    Self-explanatory. - -
    Too many neighbors in CNA for %d atoms - -
    More than the maximum # of neighbors was found multiple times. This -was unexpected. - -
    Triclinic box skew is large - -
    The displacement in a skewed direction is normally required to be less -than half the box length in that dimension. E.g. the xy tilt must be -between -half and +half of the x box length. You have relaxed the -constraint using the box tilt command, but the warning means that a -LAMMPS simulation may be inefficient as a result. - -
    Use special bonds = 0,1,1 with bond style fene - -
    Most FENE models need this setting for the special_bonds command. - -
    Use special bonds = 0,1,1 with bond style fene/expand - -
    Most FENE models need this setting for the special_bonds command. - -
    Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions - -
    This is likely not what you want to do. The exclusion settings will -eliminate neighbors in the neighbor list, which the manybody potential -needs to calculated its terms correctly. - -
    Using compute temp/deform with inconsistent fix deform remap option - -
    Fix nvt/sllod assumes deforming atoms have a velocity profile provided -by "remap v" or "remap none" as a fix deform option. - -
    Using compute temp/deform with no fix deform defined - -
    This is probably an error, since it makes little sense to use -compute temp/deform in this case. - -
    Using fix srd with box deformation but no SRD thermostat - -
    The deformation will heat the SRD particles so this can -be dangerous. - -
    Using kspace solver on system with no charge - -
    Self-explanatory. - -
    Using largest cut-off for lj/long/dipole/long long long - -
    Self-explanatory. - -
    Using largest cutoff for buck/long/coul/long - -
    Self-exlanatory. - -
    Using largest cutoff for lj/long/coul/long - -
    Self-explanatory. - -
    Using largest cutoff for pair_style lj/long/tip4p/long - -
    Self-explanatory. - -
    Using package gpu without any pair style defined - -
    Self-explanatory. - -
    Using pair tail corrections with nonperiodic system - -
    This is probably a bogus thing to do, since tail corrections are -computed by integrating the density of a periodic system out to -infinity. - - -
    - diff --git a/doc/doc2/Section_example.html b/doc/doc2/Section_example.html deleted file mode 100644 index e8b392a129..0000000000 --- a/doc/doc2/Section_example.html +++ /dev/null @@ -1,132 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
    - - - - - - -
    - -

    7. Example problems -

    -

    The LAMMPS distribution includes an examples sub-directory with -several sample problems. Each problem is in a sub-directory of its -own. Most are 2d models so that they run quickly, requiring at most a -couple of minutes to run on a desktop machine. Each problem has an -input script (in.*) and produces a log file (log.*) and dump file -(dump.*) when it runs. Some use a data file (data.*) of initial -coordinates as additional input. A few sample log file outputs on -different machines and different numbers of processors are included in -the directories to compare your answers to. E.g. a log file like -log.crack.foo.P means it ran on P processors of machine "foo". -

    -

    For examples that use input data files, many of them were produced by -Pizza.py or setup tools described in the -Additional Tools section of the LAMMPS -documentation and provided with the LAMMPS distribution. -

    -

    If you uncomment the dump command in the input script, a -text dump file will be produced, which can be animated by various -visualization programs. It can -also be animated using the xmovie tool described in the Additional -Tools section of the LAMMPS documentation. -

    -

    If you uncomment the dump image command in the input -script, and assuming you have built LAMMPS with a JPG library, JPG -snapshot images will be produced when the simulation runs. They can -be quickly post-processed into a movie using commands described on the -dump image doc page. -

    -

    Animations of many of these examples can be viewed on the Movies -section of the LAMMPS WWW Site. -

    -

    These are the sample problems in the examples sub-directories: -

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    balance dynamic load balancing, 2d system
    body body particles, 2d system
    colloid big colloid particles in a small particle solvent, 2d system
    comb models using the COMB potential
    crack crack propagation in a 2d solid
    cuda use of the USER-CUDA package for GPU acceleration
    dipole point dipolar particles, 2d system
    dreiding methanol via Dreiding FF
    eim NaCl using the EIM potential
    ellipse ellipsoidal particles in spherical solvent, 2d system
    flow Couette and Poiseuille flow in a 2d channel
    friction frictional contact of spherical asperities between 2d surfaces
    gpu use of the GPU package for GPU acceleration
    hugoniostat Hugoniostat shock dynamics
    indent spherical indenter into a 2d solid
    intel use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
    kim use of potentials in Knowledge Base for Interatomic Models (KIM)
    line line segment particles in 2d rigid bodies
    meam MEAM test for SiC and shear (same as shear examples)
    melt rapid melt of 3d LJ system
    micelle self-assembly of small lipid-like molecules into 2d bilayers
    min energy minimization of 2d LJ melt
    msst MSST shock dynamics
    nb3b use of nonbonded 3-body harmonic pair style
    neb nudged elastic band (NEB) calculation for barrier finding
    nemd non-equilibrium MD of 2d sheared system
    obstacle flow around two voids in a 2d channel
    peptide dynamics of a small solvated peptide chain (5-mer)
    peri Peridynamic model of cylinder impacted by indenter
    pour pouring of granular particles into a 3d box, then chute flow
    prd parallel replica dynamics of vacancy diffusion in bulk Si
    qeq use of the QEQ pacakge for charge equilibration
    reax RDX and TATB models using the ReaxFF
    rigid rigid bodies modeled as independent or coupled
    shear sideways shear applied to 2d solid, with and without a void
    snap NVE dynamics for BCC tantalum crystal using SNAP potential
    srd stochastic rotation dynamics (SRD) particles as solvent
    tad temperature-accelerated dynamics of vacancy diffusion in bulk Si
    tri triangular particles in rigid bodies -
    - -

    vashishta: models using the Vashishta potential -

    -

    Here is how you might run and visualize one of the sample problems: -

    -
    cd indent
-cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux -in in.indent            # run the problem 
-
    -

    Running the simulation produces the files dump.indent and -log.lammps. You can visualize the dump file as follows: -

    -
    ../../tools/xmovie/xmovie -scale dump.indent 
-
    -

    If you uncomment the dump image line(s) in the input -script a series of JPG images will be produced by the run. These can -be viewed individually or turned into a movie or animated by tools -like ImageMagick or QuickTime or various Windows-based tools. See the -dump image doc page for more details. E.g. this -Imagemagick command would create a GIF file suitable for viewing in a -browser. -

    -
    % convert -loop 1 *.jpg foo.gif 
-
    -
    - -

    There is also a COUPLE directory with examples of how to use LAMMPS as -a library, either by itself or in tandem with another code or library. -See the COUPLE/README file to get started. -

    -

    There is also an ELASTIC directory with an example script for -computing elastic constants at zero temperature, using an Si example. See -the ELASTIC/in.elastic file for more info. -

    -

    There is also an ELASTIC_T directory with an example script for -computing elastic constants at finite temperature, using an Si example. See -the ELASTIC_T/in.elastic file for more info. -

    -

    There is also a USER directory which contains subdirectories of -user-provided examples for user packages. See the README files in -those directories for more info. See the -Section_start.html file for more info about user -packages. -

    - diff --git a/doc/doc2/Section_history.html b/doc/doc2/Section_history.html deleted file mode 100644 index d827db95e7..0000000000 --- a/doc/doc2/Section_history.html +++ /dev/null @@ -1,129 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands - Next -Section -
    - - - - - - -
    - -

    13. Future and history -

    -

    This section lists features we plan to add to LAMMPS, features of -previous versions of LAMMPS, and features of other parallel molecular -dynamics codes our group has distributed. -

    -13.1 Coming attractions
    -13.2 Past versions
    - -
    - -
    - -

    13.1 Coming attractions -

    -

    The Wish list link on the -LAMMPS WWW page gives a list of features we are hoping to add to -LAMMPS in the future, including contact names of individuals you can -email if you are interested in contributing to the developement or -would be a future user of that feature. -

    -

    You can also send email to the -developers if you want to add -your wish to the list. -

    -
    - -

    13.2 Past versions -

    -

    LAMMPS development began in the mid 1990s under a cooperative research -& development agreement (CRADA) between two DOE labs (Sandia and LLNL) -and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was -to develop a large-scale parallel classical MD code; the coding effort -was led by Steve Plimpton at Sandia. -

    -

    After the CRADA ended, a final F77 version, LAMMPS 99, was -released. As development of LAMMPS continued at Sandia, its memory -management was converted to F90; a final F90 version was released as -LAMMPS 2001. -

    -

    The current LAMMPS is a rewrite in C++ and was first publicly released -as an open source code in 2004. It includes many new features beyond -those in LAMMPS 99 or 2001. It also includes features from older -parallel MD codes written at Sandia, namely ParaDyn, Warp, and -GranFlow (see below). -

    -

    In late 2006 we began merging new capabilities into LAMMPS that were -developed by Aidan Thompson at Sandia for his MD code GRASP, which has -a parallel framework similar to LAMMPS. Most notably, these have -included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF - -and the associated charge-equilibration routines needed for ReaxFF. -

    -

    The History link on the -LAMMPS WWW page gives a timeline of features added to the -C++ open-source version of LAMMPS over the last several years. -

    -

    These older codes are available for download from the LAMMPS WWW -site, except for Warp & GranFlow which were primarily used -internally. A brief listing of their features is given here. -

    -

    LAMMPS 2001 -

    -
    • F90 + MPI -
    • dynamic memory -
    • spatial-decomposition parallelism -
    • NVE, NVT, NPT, NPH, rRESPA integrators -
    • LJ and Coulombic pairwise force fields -
    • all-atom, united-atom, bead-spring polymer force fields -
    • CHARMM-compatible force fields -
    • class 2 force fields -
    • 3d/2d Ewald & PPPM -
    • various force and temperature constraints -
    • SHAKE -
    • Hessian-free truncated-Newton minimizer -
    • user-defined diagnostics -
    -

    LAMMPS 99 -

    -
    • F77 + MPI -
    • static memory allocation -
    • spatial-decomposition parallelism -
    • most of the LAMMPS 2001 features with a few exceptions -
    • no 2d Ewald & PPPM -
    • molecular force fields are missing a few CHARMM terms -
    • no SHAKE -
    -

    Warp -

    -
    • F90 + MPI -
    • spatial-decomposition parallelism -
    • embedded atom method (EAM) metal potentials + LJ -
    • lattice and grain-boundary atom creation -
    • NVE, NVT integrators -
    • boundary conditions for applying shear stresses -
    • temperature controls for actively sheared systems -
    • per-atom energy and centro-symmetry computation and output -
    -

    ParaDyn -

    -
    • F77 + MPI -
    • atom- and force-decomposition parallelism -
    • embedded atom method (EAM) metal potentials -
    • lattice atom creation -
    • NVE, NVT, NPT integrators -
    • all serial DYNAMO features for controls and constraints -
    -

    GranFlow -

    -
    • F90 + MPI -
    • spatial-decomposition parallelism -
    • frictional granular potentials -
    • NVE integrator -
    • boundary conditions for granular flow and packing and walls -
    • particle insertion -
    - diff --git a/doc/doc2/Section_howto.html b/doc/doc2/Section_howto.html deleted file mode 100644 index 4aa8cabb67..0000000000 --- a/doc/doc2/Section_howto.html +++ /dev/null @@ -1,2840 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
    - - - - - - -
    - -

    6. How-to discussions -

    -

    This section describes how to perform common tasks using LAMMPS. -

    -6.1 Restarting a simulation
    -6.2 2d simulations
    -6.3 CHARMM, AMBER, and DREIDING force fields
    -6.4 Running multiple simulations from one input script
    -6.5 Multi-replica simulations
    -6.6 Granular models
    -6.7 TIP3P water model
    -6.8 TIP4P water model
    -6.9 SPC water model
    -6.10 Coupling LAMMPS to other codes
    -6.11 Visualizing LAMMPS snapshots
    -6.12 Triclinic (non-orthogonal) simulation boxes
    -6.13 NEMD simulations
    -6.14 Finite-size spherical and aspherical particles
    -6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
    -6.16 Thermostatting, barostatting and computing temperature
    -6.17 Walls
    -6.18 Elastic constants
    -6.19 Library interface to LAMMPS
    -6.20 Calculating thermal conductivity
    -6.21 Calculating viscosity
    -6.22 Calculating a diffusion coefficient
    -6.23 Using chunks to calculate system properties
    -6.24 Setting parameters for the kspace_style pppm/disp command
    -6.25 Polarizable models
    -6.26 Adiabatic core/shell model
    -6.27 Drude induced dipoles
    - -

    The example input scripts included in the LAMMPS distribution and -highlighted in Section_example also show how to -setup and run various kinds of simulations. -

    -
    - -
    - -

    6.1 Restarting a simulation -

    -

    There are 3 ways to continue a long LAMMPS simulation. Multiple -run commands can be used in the same input script. Each -run will continue from where the previous run left off. Or binary -restart files can be saved to disk using the restart -command. At a later time, these binary files can be read via a -read_restart command in a new script. Or they can -be converted to text data files using the -r command-line -switch and read by a -read_data command in a new script. -

    -

    Here we give examples of 2 scripts that read either a binary restart -file or a converted data file and then issue a new run command to -continue where the previous run left off. They illustrate what -settings must be made in the new script. Details are discussed in the -documentation for the read_restart and -read_data commands. -

    -

    Look at the in.chain input script provided in the bench directory -of the LAMMPS distribution to see the original script that these 2 -scripts are based on. If that script had the line -

    -
    restart	        50 tmp.restart 
-
    -

    added to it, it would produce 2 binary restart files (tmp.restart.50 -and tmp.restart.100) as it ran. -

    -

    This script could be used to read the 1st restart file and re-run the -last 50 timesteps: -

    -
    read_restart	tmp.restart.50 
-
    -
    neighbor	0.4 bin
-neigh_modify	every 1 delay 1 
-
    -
    fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297 
-
    -
    timestep	0.012 
-
    -
    run		50 
-
    -

    Note that the following commands do not need to be repeated because -their settings are included in the restart file: units, atom_style, -special_bonds, pair_style, bond_style. However these commands do -need to be used, since their settings are not in the restart file: -neighbor, fix, timestep. -

    -

    If you actually use this script to perform a restarted run, you will -notice that the thermodynamic data match at step 50 (if you also put a -"thermo 50" command in the original script), but do not match at step -100. This is because the fix langevin command -uses random numbers in a way that does not allow for perfect restarts. -

    -

    As an alternate approach, the restart file could be converted to a data -file as follows: -

    -
    lmp_g++ -r tmp.restart.50 tmp.restart.data 
-
    -

    Then, this script could be used to re-run the last 50 steps: -

    -
    units		lj
-atom_style	bond
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-bond_style	fene
-special_bonds   0.0 1.0 1.0 
-
    -
    read_data	tmp.restart.data 
-
    -
    neighbor	0.4 bin
-neigh_modify	every 1 delay 1 
-
    -
    fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297 
-
    -
    timestep	0.012 
-
    -
    reset_timestep	50
-run		50 
-
    -

    Note that nearly all the settings specified in the original in.chain -script must be repeated, except the pair_coeff and bond_coeff -commands since the new data file lists the force field coefficients. -Also, the reset_timestep command is used to tell -LAMMPS the current timestep. This value is stored in restart files, -but not in data files. -

    -
    - -

    6.2 2d simulations -

    -

    Use the dimension command to specify a 2d simulation. -

    -

    Make the simulation box periodic in z via the boundary -command. This is the default. -

    -

    If using the create box command to define a -simulation box, set the z dimensions narrow, but finite, so that the -create_atoms command will tile the 3d simulation box with a single z -plane of atoms - e.g. -

    -
    create box 1 -10 10 -10 10 -0.25 0.25 
-
    -

    If using the read data command to read in a file of -atom coordinates, set the "zlo zhi" values to be finite but narrow, -similar to the create_box command settings just described. For each -atom in the file, assign a z coordinate so it falls inside the -z-boundaries of the box - e.g. 0.0. -

    -

    Use the fix enforce2d command as the last -defined fix to insure that the z-components of velocities and forces -are zeroed out every timestep. The reason to make it the last fix is -so that any forces induced by other fixes will be zeroed out. -

    -

    Many of the example input scripts included in the LAMMPS distribution -are for 2d models. -

    -

    IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size -spheres, as opposed to point particles. In 2d, the particles will -still be spheres, not disks, meaning their moment of inertia will be -the same as in 3d. -

    -
    - -

    6.3 CHARMM, AMBER, and DREIDING force fields -

    -

    A force field has 2 parts: the formulas that define it and the -coefficients used for a particular system. Here we only discuss -formulas implemented in LAMMPS that correspond to formulas commonly -used in the CHARMM, AMBER, and DREIDING force fields. Setting -coefficients is done in the input data file via the -read_data command or in the input script with -commands like pair_coeff or -bond_coeff. See Section_tools -for additional tools that can use CHARMM or AMBER to assign force -field coefficients and convert their output into LAMMPS input. -

    -

    See (MacKerell) for a description of the CHARMM force -field. See (Cornell) for a description of the AMBER force -field. -

    - - - - -

    These style choices compute force field formulas that are consistent -with common options in CHARMM or AMBER. See each command's -documentation for the formula it computes. -

    - - -

    DREIDING is a generic force field developed by the Goddard -group at Caltech and is useful for -predicting structures and dynamics of organic, biological and -main-group inorganic molecules. The philosophy in DREIDING is to use -general force constants and geometry parameters based on simple -hybridization considerations, rather than individual force constants -and geometric parameters that depend on the particular combinations of -atoms involved in the bond, angle, or torsion terms. DREIDING has an -explicit hydrogen bond term to describe -interactions involving a hydrogen atom on very electronegative atoms -(N, O, F). -

    -

    See (Mayo) for a description of the DREIDING force field -

    -

    These style choices compute force field formulas that are consistent -with the DREIDING force field. See each command's -documentation for the formula it computes. -

    - - - - - - -
    - -

    6.4 Running multiple simulations from one input script -

    -

    This can be done in several ways. See the documentation for -individual commands for more details on how these examples work. -

    -

    If "multiple simulations" means continue a previous simulation for -more timesteps, then you simply use the run command -multiple times. For example, this script -

    -
    units lj
-atom_style atomic
-read_data data.lj
-run 10000
-run 10000
-run 10000
-run 10000
-run 10000 
-
    -

    would run 5 successive simulations of the same system for a total of -50,000 timesteps. -

    -

    If you wish to run totally different simulations, one after the other, -the clear command can be used in between them to -re-initialize LAMMPS. For example, this script -

    -
    units lj
-atom_style atomic
-read_data data.lj
-run 10000
-clear
-units lj
-atom_style atomic
-read_data data.lj.new
-run 10000 
-
    -

    would run 2 independent simulations, one after the other. -

    -

    For large numbers of independent simulations, you can use -variables and the next and -jump commands to loop over the same input script -multiple times with different settings. For example, this -script, named in.polymer -

    -
    variable d index run1 run2 run3 run4 run5 run6 run7 run8
-shell cd $d
-read_data data.polymer
-run 10000
-shell cd ..
-clear
-next d
-jump in.polymer 
-
    -

    would run 8 simulations in different directories, using a data.polymer -file in each directory. The same concept could be used to run the -same system at 8 different temperatures, using a temperature variable -and storing the output in different log and dump files, for example -

    -
    variable a loop 8
-variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
-log log.$a
-read data.polymer
-velocity all create $t 352839
-fix 1 all nvt $t $t 100.0
-dump 1 all atom 1000 dump.$a
-run 100000
-clear
-next t
-next a
-jump in.polymer 
-
    -

    All of the above examples work whether you are running on 1 or -multiple processors, but assumed you are running LAMMPS on a single -partition of processors. LAMMPS can be run on multiple partitions via -the "-partition" command-line switch as described in this -section of the manual. -

    -

    In the last 2 examples, if LAMMPS were run on 3 partitions, the same -scripts could be used if the "index" and "loop" variables were -replaced with universe-style variables, as described in the -variable command. Also, the "next t" and "next a" -commands would need to be replaced with a single "next a t" command. -With these modifications, the 8 simulations of each script would run -on the 3 partitions one after the other until all were finished. -Initially, 3 simulations would be started simultaneously, one on each -partition. When one finished, that partition would then start -the 4th simulation, and so forth, until all 8 were completed. -

    -
    - -

    6.5 Multi-replica simulations -

    -

    Several commands in LAMMPS run mutli-replica simulations, meaning -that multiple instances (replicas) of your simulation are run -simultaneously, with small amounts of data exchanged between replicas -periodically. -

    -

    These are the relevant commands: -

    -
    • neb for nudged elastic band calculations -
    • prd for parallel replica dynamics -
    • tad for temperature accelerated dynamics -
    • temper for parallel tempering -
    • fix pimd for path-integral molecular dynamics (PIMD) -
    -

    NEB is a method for finding transition states and barrier energies. -PRD and TAD are methods for performing accelerated dynamics to find -and perform infrequent events. Parallel tempering or replica exchange -runs different replicas at a series of temperature to facilitate -rare-event sampling. -

    -

    These commands can only be used if LAMMPS was built with the REPLICA -package. See the Making LAMMPS section -for more info on packages. -

    -

    PIMD runs different replicas whose individual particles are coupled -together by springs to model a system or ring-polymers. -

    -

    This commands can only be used if LAMMPS was built with the USER-MISC -package. See the Making LAMMPS section -for more info on packages. -

    -

    In all these cases, you must run with one or more processors per -replica. The processors assigned to each replica are determined at -run-time by using the -partition command-line -switch to launch LAMMPS on multiple -partitions, which in this context are the same as replicas. E.g. -these commands: -

    -
    mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
-mpirun -np 8 lmp_linux -partition 8x1 -in in.neb 
-
    -

    would each run 8 replicas, on either 16 or 8 processors. Note the use -of the -in command-line switch to specify -the input script which is required when running in multi-replica mode. -

    -

    Also note that with MPI installed on a machine (e.g. your desktop), -you can run on more (virtual) processors than you have physical -processors. Thus the above commands could be run on a -single-processor (or few-processor) desktop so that you can run -a multi-replica simulation on more replicas than you have -physical processors. -

    -
    - -

    6.6 Granular models -

    -

    Granular system are composed of spherical particles with a diameter, -as opposed to point particles. This means they have an angular -velocity and torque can be imparted to them to cause them to rotate. -

    -

    To run a simulation of a granular model, you will want to use -the following commands: -

    - -

    This compute -

    - -

    calculates rotational kinetic energy which can be output with -thermodynamic info. -

    -

    Use one of these 3 pair potentials, which compute forces and torques -between interacting pairs of particles: -

    - -

    These commands implement fix options specific to granular systems: -

    - -

    The fix style freeze zeroes both the force and torque of frozen -atoms, and should be used for granular system instead of the fix style -setforce. -

    -

    For computational efficiency, you can eliminate needless pairwise -computations between frozen atoms by using this command: -

    - -
    - -

    6.7 TIP3P water model -

    -

    The TIP3P water model as implemented in CHARMM -(MacKerell) specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the fix shake command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -harmonic and an angle style of harmonic or charmm should also be -used. -

    -

    These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP3P-CHARMM model with a -cutoff. The K values can be used if a flexible TIP3P model (without -fix shake) is desired. If the LJ epsilon and sigma for HH and OH are -set to 0.0, it corresponds to the original 1983 TIP3P model -(Jorgensen). -

    -

    O mass = 15.9994
    -H mass = 1.008
    -O charge = -0.834
    -H charge = 0.417
    -LJ epsilon of OO = 0.1521
    -LJ sigma of OO = 3.1507
    -LJ epsilon of HH = 0.0460
    -LJ sigma of HH = 0.4000
    -LJ epsilon of OH = 0.0836
    -LJ sigma of OH = 1.7753
    -K of OH bond = 450
    -r0 of OH bond = 0.9572
    -K of HOH angle = 55
    -theta of HOH angle = 104.52
    -

    -

    These are the parameters to use for TIP3P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS), see (Price) for -details: -

    -

    O mass = 15.9994
    -H mass = 1.008
    -O charge = -0.830
    -H charge = 0.415
    -LJ epsilon of OO = 0.102
    -LJ sigma of OO = 3.188
    -LJ epsilon, sigma of OH, HH = 0.0
    -K of OH bond = 450
    -r0 of OH bond = 0.9572
    -K of HOH angle = 55
    -theta of HOH angle = 104.52
    -

    -

    Wikipedia also has a nice article on water -models. -

    -
    - -

    6.8 TIP4P water model -

    -

    The four-point TIP4P rigid water model extends the traditional -three-point TIP3P model by adding an additional site, usually -massless, where the charge associated with the oxygen atom is placed. -This site M is located at a fixed distance away from the oxygen along -the bisector of the HOH bond angle. A bond style of harmonic and an -angle style of harmonic or charmm should also be used. -

    -

    A TIP4P model is run with LAMMPS using either this command -for a cutoff model: -

    -

    pair_style lj/cut/tip4p/cut -

    -

    or these two commands for a long-range model: -

    - -

    For both models, the bond lengths and bond angles should be held fixed -using the fix shake command. -

    -

    These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP4P model with a cutoff -(Jorgensen). Note that the OM distance is specified in -the pair_style command, not as part of the pair -coefficients. -

    -

    O mass = 15.9994
    -H mass = 1.008
    -O charge = -1.040
    -H charge = 0.520
    -r0 of OH bond = 0.9572
    -theta of HOH angle = 104.52
    -OM distance = 0.15
    -LJ epsilon of O-O = 0.1550
    -LJ sigma of O-O = 3.1536
    -LJ epsilon, sigma of OH, HH = 0.0
    -Coulombic cutoff = 8.5
    -

    -

    For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); -http://dx.doi.org/10.1063/1.1931662) these values can be used: -

    -

    O mass = 15.9994
    -H mass = 1.008
    -O charge = -1.1794
    -H charge = 0.5897
    -r0 of OH bond = 0.9572
    -theta of HOH angle = 104.52
    -OM distance = 0.1577
    -LJ epsilon of O-O = 0.21084
    -LJ sigma of O-O = 3.1668
    -LJ epsilon, sigma of OH, HH = 0.0
    -Coulombic cutoff = 8.5
    -

    -

    For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); -http://dx.doi.org/10.1063/1.2121687), these values can be used: -

    -

    O mass = 15.9994
    -H mass = 1.008
    -O charge = -1.1128
    -H charge = 0.5564
    -r0 of OH bond = 0.9572
    -theta of HOH angle = 104.52
    -OM distance = 0.1546
    -LJ epsilon of O-O = 0.1852
    -LJ sigma of O-O = 3.1589
    -LJ epsilon, sigma of OH, HH = 0.0
    -Coulombic cutoff = 8.5
    -

    -

    These are the parameters to use for TIP4P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS): -

    -

    O mass = 15.9994
    -H mass = 1.008
    -O charge = -1.0484
    -H charge = 0.5242
    -r0 of OH bond = 0.9572
    -theta of HOH angle = 104.52
    -OM distance = 0.1250
    -LJ epsilon of O-O = 0.16275
    -LJ sigma of O-O = 3.16435
    -LJ epsilon, sigma of OH, HH = 0.0
    -

    -

    Note that the when using the TIP4P pair style, the neighobr list -cutoff for Coulomb interactions is effectively extended by a distance -2 * (OM distance), to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*(OM distance), to shrink the size of the neighbor list. -This leads to slightly larger cost for the long-range calculation, so -you can test the trade-off for your model. The OM distance and the LJ -and Coulombic cutoffs are set in the pair_style -lj/cut/tip4p/long command. -

    -

    Wikipedia also has a nice article on water -models. -

    -
    - -

    6.9 SPC water model -

    -

    The SPC water model specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the fix shake command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -harmonic and an angle style of harmonic or charmm should also be -used. -

    -

    These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid SPC model. -

    -

    O mass = 15.9994
    -H mass = 1.008
    -O charge = -0.820
    -H charge = 0.410
    -LJ epsilon of OO = 0.1553
    -LJ sigma of OO = 3.166
    -LJ epsilon, sigma of OH, HH = 0.0
    -r0 of OH bond = 1.0
    -theta of HOH angle = 109.47
    -

    -

    Note that as originally proposed, the SPC model was run with a 9 -Angstrom cutoff for both LJ and Coulommbic terms. It can also be used -with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing -any of the parameters above, though it becomes a different model in -that mode of usage. -

    -

    The SPC/E (extended) water model is the same, except -the partial charge assignemnts change: -

    -

    O charge = -0.8476
    -H charge = 0.4238
    -

    -

    See the (Berendsen) reference for more details on both -the SPC and SPC/E models. -

    -

    Wikipedia also has a nice article on water -models. -

    -
    - -

    6.10 Coupling LAMMPS to other codes -

    -

    LAMMPS is designed to allow it to be coupled to other codes. For -example, a quantum mechanics code might compute forces on a subset of -atoms and pass those forces to LAMMPS. Or a continuum finite element -(FE) simulation might use atom positions as boundary conditions on FE -nodal points, compute a FE solution, and return interpolated forces on -MD atoms. -

    -

    LAMMPS can be coupled to other codes in at least 3 ways. Each has -advantages and disadvantages, which you'll have to think about in the -context of your application. -

    -

    (1) Define a new fix command that calls the other code. In -this scenario, LAMMPS is the driver code. During its timestepping, -the fix is invoked, and can make library calls to the other code, -which has been linked to LAMMPS as a library. This is the way the -POEMS package that performs constrained rigid-body motion on -groups of atoms is hooked to LAMMPS. See the -fix_poems command for more details. See this -section of the documentation for info on how to add -a new fix to LAMMPS. -

    - - -

    (2) Define a new LAMMPS command that calls the other code. This is -conceptually similar to method (1), but in this case LAMMPS and the -other code are on a more equal footing. Note that now the other code -is not called during the timestepping of a LAMMPS run, but between -runs. The LAMMPS input script can be used to alternate LAMMPS runs -with calls to the other code, invoked via the new command. The -run command facilitates this with its every option, which -makes it easy to run a few steps, invoke the command, run a few steps, -invoke the command, etc. -

    -

    In this scenario, the other code can be called as a library, as in -(1), or it could be a stand-alone code, invoked by a system() call -made by the command (assuming your parallel machine allows one or more -processors to start up another program). In the latter case the -stand-alone code could communicate with LAMMPS thru files that the -command writes and reads. -

    -

    See Section_modify of the documentation for how -to add a new command to LAMMPS. -

    -

    (3) Use LAMMPS as a library called by another code. In this case the -other code is the driver and calls LAMMPS as needed. Or a wrapper -code could link and call both LAMMPS and another code as libraries. -Again, the run command has options that allow it to be -invoked with minimal overhead (no setup or clean-up) if you wish to do -multiple short runs, driven by another program. -

    -

    Examples of driver codes that call LAMMPS as a library are included in -the examples/COUPLE directory of the LAMMPS distribution; see -examples/COUPLE/README for more details: -

    -
    • simple: simple driver programs in C++ and C which invoke LAMMPS as a -library - -
    • lammps_quest: coupling of LAMMPS and Quest, to run classical -MD with quantum forces calculated by a density functional code - -
    • lammps_spparks: coupling of LAMMPS and SPPARKS, to couple -a kinetic Monte Carlo model for grain growth using MD to calculate -strain induced across grain boundaries -
    - - - - -

    This section of the documentation -describes how to build LAMMPS as a library. Once this is done, you -can interface with LAMMPS either via C++, C, Fortran, or Python (or -any other language that supports a vanilla C-like interface). For -example, from C++ you could create one (or more) "instances" of -LAMMPS, pass it an input script to process, or execute individual -commands, all by invoking the correct class methods in LAMMPS. From C -or Fortran you can make function calls to do the same things. See -Section_python of the manual for a description -of the Python wrapper provided with LAMMPS that operates through the -LAMMPS library interface. -

    -

    The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See Section_howto 19 of the -manual for a description of the interface and how to extend it for -your needs. -

    -

    Note that the lammps_open() function that creates an instance of -LAMMPS takes an MPI communicator as an argument. This means that -instance of LAMMPS will run on the set of processors in the -communicator. Thus the calling code can run LAMMPS on all or a subset -of processors. For example, a wrapper script might decide to -alternate between LAMMPS and another code, allowing them both to run -on all the processors. Or it might allocate half the processors to -LAMMPS and half to the other code and run both codes simultaneously -before syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. -

    -
    - -

    6.11 Visualizing LAMMPS snapshots -

    -

    LAMMPS itself does not do visualization, but snapshots from LAMMPS -simulations can be visualized (and analyzed) in a variety of ways. -

    -

    LAMMPS snapshots are created by the dump command which can -create files in several formats. The native LAMMPS dump format is a -text file (see "dump atom" or "dump custom") which can be visualized -by the xmovie program, included with the -LAMMPS package. This produces simple, fast 2d projections of 3d -systems, and can be useful for rapid debugging of simulation geometry -and atom trajectories. -

    -

    Several programs included with LAMMPS as auxiliary tools can convert -native LAMMPS dump files to other formats. See the -Section_tools doc page for details. The first is -the ch2lmp tool, which contains a -lammps2pdb Perl script which converts LAMMPS dump files into PDB -files. The second is the lmp2arc tool which -converts LAMMPS dump files into Accelrys' Insight MD program files. -The third is the lmp2cfg tool which converts -LAMMPS dump files into CFG files which can be read into the -AtomEye visualizer. -

    -

    A Python-based toolkit distributed by our group can read native LAMMPS -dump files, including custom dump files with additional columns of -user-specified atom information, and convert them to various formats -or pipe them into visualization software directly. See the Pizza.py -WWW site for details. Specifically, Pizza.py can convert -LAMMPS dump files into PDB, XYZ, Ensight, and VTK formats. -Pizza.py can pipe LAMMPS dump files directly into the Raster3d and -RasMol visualization programs. Pizza.py has tools that do interactive -3d OpenGL visualization and one that creates SVG images of dump file -snapshots. -

    -

    LAMMPS can create XYZ files directly (via "dump xyz") which is a -simple text-based file format used by many visualization programs -including VMD. -

    -

    LAMMPS can create DCD files directly (via "dump dcd") which can be -read by VMD in conjunction with a CHARMM PSF file. Using this -form of output avoids the need to convert LAMMPS snapshots to PDB -files. See the dump command for more information on DCD -files. -

    -

    LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS -file format which can also be read by VMD for visualization. -See the dump command for more information on XTC files. -

    - - - - - - - - -
    - -

    6.12 Triclinic (non-orthogonal) simulation boxes -

    -

    By default, LAMMPS uses an orthogonal simulation box to encompass the -particles. The boundary command sets the boundary -conditions of the box (periodic, non-periodic, etc). The orthogonal -box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors -starting from the origin given by a = (xhi-xlo,0,0); b = -(0,yhi-ylo,0); c = (0,0,zhi-zlo). The 6 parameters -(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the create_box or -read_data or read_restart -commands. Additionally, LAMMPS defines box size parameters lx,ly,lz -where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the thermo_style -custom command. -

    -

    LAMMPS also allows simulations to be performed in triclinic -(non-orthogonal) simulation boxes shaped as a parallelepiped with -triclinic symmetry. The parallelepiped has its "origin" at -(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the -origin given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = -(xz,yz,zhi-zlo). xy,xz,yz can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. In LAMMPS the triclinic -simulation box edge vectors a, b, and c cannot be arbitrary -vectors. As indicated, a must lie on the positive x axis. b must -lie in the xy plane, with strictly positive y component. c may have -any orientation with strictly positive z component. The requirement -that a, b, and c have strictly positive x, y, and z components, -respectively, ensures that a, b, and c form a complete -right-handed basis. These restrictions impose no loss of generality, -since it is possible to rotate/invert any set of 3 crystal basis -vectors so that they conform to the restrictions. -

    -

    For example, assume that the 3 vectors A,B,C are the edge -vectors of a general parallelepiped, where there is no restriction on -A,B,C other than they form a complete right-handed basis i.e. -A x B . C > 0. The equivalent LAMMPS a,b,c are a linear -rotation of A, B, and C and can be computed as follows: -

    -
    -
    -

    where A = |A| indicates the scalar length of A. The ^ hat symbol -indicates the corresponding unit vector. beta and gamma are angles -between the vectors described below. Note that by construction, -a, b, and c have strictly positive x, y, and z components, respectively. -If it should happen that -A, B, and C form a left-handed basis, then the above equations -are not valid for c. In this case, it is necessary -to first apply an inversion. This can be achieved -by interchanging two basis vectors or by changing the sign of one of them. -

    -

    For consistency, the same rotation/inversion applied to the basis vectors -must also be applied to atom positions, velocities, -and any other vector quantities. -This can be conveniently achieved by first converting to -fractional coordinates in the -old basis and then converting to distance coordinates in the new basis. -The transformation is given by the following equation: -

    -
    -
    -

    where V is the volume of the box, X is the original vector quantity and -x is the vector in the LAMMPS basis. -

    -

    There is no requirement that a triclinic box be periodic in any -dimension, though it typically should be in at least the 2nd dimension -of the tilt (y in xy) if you want to enforce a shift in periodic -boundary conditions across that boundary. Some commands that work -with triclinic boxes, e.g. the fix deform and fix -npt commands, require periodicity or non-shrink-wrap -boundary conditions in specific dimensions. See the command doc pages -for details. -

    -

    The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simluation box is created. This happens in one of 3 ways. -If the create_box command is used with a region of -style prism, then a triclinic box is setup. See the -region command for details. If the -read_data command is used to define the simulation -box, and the header of the data file contains a line with the "xy xz -yz" keyword, then a triclinic box is setup. See the -read_data command for details. Finally, if the -read_restart command reads a restart file which -was written from a simulation using a triclinic box, then a triclinic -box will be setup for the restarted simulation. -

    -

    Note that you can define a triclinic box with all 3 tilt factors = -0.0, so that it is initially orthogonal. This is necessary if the box -will become non-orthogonal, e.g. due to the fix npt or -fix deform commands. Alternatively, you can use the -change_box command to convert a simulation box from -orthogonal to triclinic and vice versa. -

    -

    As with orthogonal boxes, LAMMPS defines triclinic box size parameters -lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. -The 9 parameters, as well as lx,ly,lz, can be output via the -thermo_style custom command. -

    -

    To avoid extremely tilted boxes (which would be computationally -inefficient), LAMMPS normally requires that no tilt factor can skew -the box more than half the distance of the parallel box length, which -is the 1st dimension in the tilt factor (x for xz). This is required -both when the simulation box is created, e.g. via the -create_box or read_data commands, -as well as when the box shape changes dynamically during a simulation, -e.g. via the fix deform or fix npt -commands. -

    -

    For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are geometrically all equivalent. If the box tilt exceeds this -limit during a dynamics run (e.g. via the fix deform -command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the fix -deform doc page for further details. -

    -

    One exception to this rule is if the 1st dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient, due to the highly skewed simulation box. -

    -

    The limitation on not creating a simulation box with a tilt factor -skewing the box more than half the distance of the parallel box length -can be overridden via the box command. Setting the tilt -keyword to large allows any tilt factors to be specified. -

    -

    Box flips that may occur using the fix deform or -fix npt commands can be turned off using the flip no -option with either of the commands. -

    -

    Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. -

    -

    Triclinic crystal structures are often defined using three lattice -constants a, b, and c, and three angles alpha, beta and -gamma. Note that in this nomenclature, the a, b, and c lattice -constants are the scalar lengths of the edge vectors a, b, and c -defined above. The relationship between these 6 quantities -(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) = -(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: -

    -
    -
    -

    The inverse relationship can be written as follows: -

    -
    -
    -

    The values of a, b, c , alpha, beta , and gamma can be printed -out or accessed by computes using the -thermo_style custom keywords -cella, cellb, cellc, cellalpha, cellbeta, cellgamma, -respectively. -

    -

    As discussed on the dump command doc page, when the BOX -BOUNDS for a snapshot is written to a dump file for a triclinic box, -an orthogonal bounding box which encloses the triclinic simulation box -is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic -box, formatted as follows: -

    -
    ITEM: BOX BOUNDS xy xz yz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz 
-
    -

    This bounding box is convenient for many visualization programs and is -calculated from the 9 triclinic box parameters -(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: -

    -
    xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
-xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
-ylo_bound = ylo + MIN(0.0,yz)
-yhi_bound = yhi + MAX(0.0,yz)
-zlo_bound = zlo
-zhi_bound = zhi 
-
    -

    These formulas can be inverted if you need to convert the bounding box -back into the triclinic box parameters, e.g. xlo = xlo_bound - -MIN(0.0,xy,xz,xy+xz). -

    -

    One use of triclinic simulation boxes is to model solid-state crystals -with triclinic symmetry. The lattice command can be -used with non-orthogonal basis vectors to define a lattice that will -tile a triclinic simulation box via the -create_atoms command. -

    -

    A second use is to run Parinello-Rahman dyanamics via the fix -npt command, which will adjust the xy, xz, yz tilt -factors to compensate for off-diagonal components of the pressure -tensor. The analalog for an energy minimization is -the fix box/relax command. -

    -

    A third use is to shear a bulk solid to study the response of the -material. The fix deform command can be used for -this purpose. It allows dynamic control of the xy, xz, yz tilt -factors as a simulation runs. This is discussed in the next section -on non-equilibrium MD (NEMD) simulations. -

    -
    - -

    6.13 NEMD simulations -

    -

    Non-equilibrium molecular dynamics or NEMD simulations are typically -used to measure a fluid's rheological properties such as viscosity. -In LAMMPS, such simulations can be performed by first setting up a -non-orthogonal simulation box (see the preceding Howto section). -

    -

    A shear strain can be applied to the simulation box at a desired -strain rate by using the fix deform command. The -fix nvt/sllod command can be used to thermostat -the sheared fluid and integrate the SLLOD equations of motion for the -system. Fix nvt/sllod uses compute -temp/deform to compute a thermal temperature -by subtracting out the streaming velocity of the shearing atoms. The -velocity profile or other properties of the fluid can be monitored via -the fix ave/spatial command. -

    -

    As discussed in the previous section on non-orthogonal simulation -boxes, the amount of tilt or skew that can be applied is limited by -LAMMPS for computational efficiency to be 1/2 of the parallel box -length. However, fix deform can continuously strain -a box by an arbitrary amount. As discussed in the fix -deform command, when the tilt value reaches a limit, -the box is flipped to the opposite limit which is an equivalent tiling -of periodic space. The strain rate can then continue to change as -before. In a long NEMD simulation these box re-shaping events may -occur many times. -

    -

    In a NEMD simulation, the "remap" option of fix -deform should be set to "remap v", since that is what -fix nvt/sllod assumes to generate a velocity -profile consistent with the applied shear strain rate. -

    -

    An alternative method for calculating viscosities is provided via the -fix viscosity command. -

    -
    - -

    6.14 Finite-size spherical and aspherical particles -

    -

    Typical MD models treat atoms or particles as point masses. Sometimes -it is desirable to have a model with finite-size particles such as -spheroids or ellipsoids or generalized aspherical bodies. The -difference is that such particles have a moment of inertia, rotational -energy, and angular momentum. Rotation is induced by torque coming -from interactions with other particles. -

    -

    LAMMPS has several options for running simulations with these kinds of -particles. The following aspects are discussed in turn: -

    -
    • atom styles -
    • pair potentials -
    • time integration -
    • computes, thermodynamics, and dump output -
    • rigid bodies composed of finite-size particles -
    -

    Example input scripts for these kinds of models are in the body, -colloid, dipole, ellipse, line, peri, pour, and tri directories of the -examples directory in the LAMMPS distribution. -

    -
    Atom styles -
    -

    There are several atom styles that allow for -definition of finite-size particles: sphere, dipole, ellipsoid, line, -tri, peri, and body. -

    -

    The sphere style defines particles that are spheriods and each -particle can have a unique diameter and mass (or density). These -particles store an angular velocity (omega) and can be acted upon by -torque. The "set" command can be used to modify the diameter and mass -of individual particles, after then are created. -

    -

    The dipole style does not actually define finite-size particles, but -is often used in conjunction with spherical particles, via a command -like -

    -
    atom_style hybrid sphere dipole 
-
    -

    This is because when dipoles interact with each other, they induce -torques, and a particle must be finite-size (i.e. have a moment of -inertia) in order to respond and rotate. See the atom_style -dipole command for details. The "set" command can be -used to modify the orientation and length of the dipole moment of -individual particles, after then are created. -

    -

    The ellipsoid style defines particles that are ellipsoids and thus can -be aspherical. Each particle has a shape, specified by 3 diameters, -and mass (or density). These particles store an angular momentum and -their orientation (quaternion), and can be acted upon by torque. They -do not store an angular velocity (omega), which can be in a different -direction than angular momentum, rather they compute it as needed. -The "set" command can be used to modify the diameter, orientation, and -mass of individual particles, after then are created. It also has a -brief explanation of what quaternions are. -

    -

    The line style defines line segment particles with two end points and -a mass (or density). They can be used in 2d simulations, and they can -be joined together to form rigid bodies which represent arbitrary -polygons. -

    -

    The tri style defines triangular particles with three corner points -and a mass (or density). They can be used in 3d simulations, and they -can be joined together to form rigid bodies which represent arbitrary -particles with a triangulated surface. -

    -

    The peri style is used with Peridynamic models and -defines particles as having a volume, that is used internally in the -pair_style peri potentials. -

    -

    The body style allows for definition of particles which can represent -complex entities, such as surface meshes of discrete points, -collections of sub-particles, deformable objects, etc. The body style -is discussed in more detail on the body doc page. -

    -

    Note that if one of these atom styles is used (or multiple styles via -the atom_style hybrid command), not all particles in -the system are required to be finite-size or aspherical. -

    -

    For example, in the ellipsoid style, if the 3 shape parameters are set -to the same value, the particle will be a sphere rather than an -ellipsoid. If the 3 shape parameters are all set to 0.0 or if the -diameter is set to 0.0, it will be a point particle. In the line or -tri style, if the lineflag or triflag is specified as 0, then it -will be a point particle. -

    -

    Some of the pair styles used to compute pairwise interactions between -finite-size particles also compute the correct interaction with point -particles as well, e.g. the interaction between a point particle and a -finite-size particle or between two point particles. If necessary, -pair_style hybrid can be used to insure the correct -interactions are computed for the appropriate style of interactions. -Likewise, using groups to partition particles (ellipsoids versus -spheres versus point particles) will allow you to use the appropriate -time integrators and temperature computations for each class of -particles. See the doc pages for various commands for details. -

    -

    Also note that for 2d simulations, atom styles sphere -and ellipsoid still use 3d particles, rather than as circular disks or -ellipses. This means they have the same moment of inertia as the 3d -object. When temperature is computed, the correct degrees of freedom -are used for rotation in a 2d versus 3d system. -

    -
    Pair potentials -
    -

    When a system with finite-size particles is defined, the particles -will only rotate and experience torque if the force field computes -such interactions. These are the various pair -styles that generate torque: -

    - -

    The granular pair styles are used with spherical particles. The -dipole pair style is used with the dipole atom style, which could be -applied to spherical or ellipsoidal particles. The GayBerne and -REsquared potentials require ellipsoidal particles, though they will -also work if the 3 shape parameters are the same (a sphere). The -Brownian and lubrication potentials are used with spherical particles. -The line, tri, and body potentials are used with line segment, -triangular, and body particles respectively. -

    -
    Time integration -
    -

    There are several fixes that perform time integration on finite-size -spherical particles, meaning the integrators update the rotational -orientation and angular velocity or angular momentum of the particles: -

    - -

    Likewise, there are 3 fixes that perform time integration on -ellipsoidal particles: -

    - -

    The advantage of these fixes is that those which thermostat the -particles include the rotational degrees of freedom in the temperature -calculation and thermostatting. The fix langevin -command can also be used with its omgea or angmom options to -thermostat the rotational degrees of freedom for spherical or -ellipsoidal particles. Other thermostatting fixes only operate on the -translational kinetic energy of finite-size particles. -

    -

    These fixes perform constant NVE time integration on line segment, -triangular, and body particles: -

    - -

    Note that for mixtures of point and finite-size particles, these -integration fixes can only be used with groups which -contain finite-size particles. -

    -
    Computes, thermodynamics, and dump output -
    -

    There are several computes that calculate the temperature or -rotational energy of spherical or ellipsoidal particles: -

    - -

    These include rotational degrees of freedom in their computation. If -you wish the thermodynamic output of temperature or pressure to use -one of these computes (e.g. for a system entirely composed of -finite-size particles), then the compute can be defined and the -thermo_modify command used. Note that by default -thermodynamic quantities will be calculated with a temperature that -only includes translational degrees of freedom. See the -thermo_style command for details. -

    -

    These commands can be used to output various attributes of finite-size -particles: -

    - -

    Attributes include the dipole moment, the angular velocity, the -angular momentum, the quaternion, the torque, the end-point and -corner-point coordinates (for line and tri particles), and -sub-particle attributes of body particles. -

    -
    Rigid bodies composed of finite-size particles -
    -

    The fix rigid command treats a collection of -particles as a rigid body, computes its inertia tensor, sums the total -force and torque on the rigid body each timestep due to forces on its -constituent particles, and integrates the motion of the rigid body. -

    -

    If any of the constituent particles of a rigid body are finite-size -particles (spheres or ellipsoids or line segments or triangles), then -their contribution to the inertia tensor of the body is different than -if they were point particles. This means the rotational dynamics of -the rigid body will be different. Thus a model of a dimer is -different if the dimer consists of two point masses versus two -spheroids, even if the two particles have the same mass. Finite-size -particles that experience torque due to their interaction with other -particles will also impart that torque to a rigid body they are part -of. -

    -

    See the "fix rigid" command for example of complex rigid-body models -it is possible to define in LAMMPS. -

    -

    Note that the fix shake command can also be used to -treat 2, 3, or 4 particles as a rigid body, but it always assumes the -particles are point masses. -

    -

    Also note that body particles cannot be modeled with the fix -rigid command. Body particles are treated by LAMMPS -as single particles, though they can store internal state, such as a -list of sub-particles. Individual body partices are typically treated -as rigid bodies, and their motion integrated with a command like fix -nve/body. Interactions between pairs of body -particles are computed via a command like pair_style -body. -

    -
    - -

    6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) -

    -

    There are four basic kinds of LAMMPS output: -

    -
    • Thermodynamic output, which is a list -of quantities printed every few timesteps to the screen and logfile. - -
    • Dump files, which contain snapshots of atoms and various -per-atom values and are written at a specified frequency. - -
    • Certain fixes can output user-specified quantities to files: fix -ave/time for time averaging, fix -ave/spatial for spatial averaging, and fix -print for single-line output of -variables. Fix print can also output to the -screen. - -
    • Restart files. -
    -

    A simulation prints one set of thermodynamic output and (optionally) -restart files. It can generate any number of dump files and fix -output files, depending on what dump and fix -commands you specify. -

    -

    As discussed below, LAMMPS gives you a variety of ways to determine -what quantities are computed and printed when the thermodynamics, -dump, or fix commands listed above perform output. Throughout this -discussion, note that users can also add their own computes and fixes -to LAMMPS which can then generate values that can -then be output with these commands. -

    -

    The following sub-sections discuss different LAMMPS command related -to output and the kind of data they operate on and produce: -

    - -
    Global/per-atom/local data -
    -

    Various output-related commands work with three different styles of -data: global, per-atom, or local. A global datum is one or more -system-wide values, e.g. the temperature of the system. A per-atom -datum is one or more values per atom, e.g. the kinetic energy of each -atom. Local datums are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. -

    -
    Scalar/vector/array data -
    -

    Global, per-atom, and local datums can each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for a "compute" or "fix" or "variable" that generates data -will specify both the style and kind of data it produces, e.g. a -per-atom vector. -

    -

    When a quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID in this case is the ID of a compute. The leading -"c_" would be replaced by "f_" for a fix, or "v_" for a variable: -

    -
    - - -
    c_ID entire scalar, vector, or array
    c_ID[I] one element of vector, one column of array
    c_ID[I][J] one element of array -
    - -

    In other words, using one bracket reduces the dimension of the data -once (vector -> scalar, array -> vector). Using two brackets reduces -the dimension twice (array -> scalar). Thus a command that uses -scalar values as input can typically also process elements of a vector -or array. -

    -
    Thermodynamic output -
    -

    The frequency and format of thermodynamic output is set by the -thermo, thermo_style, and -thermo_modify commands. The -thermo_style command also specifies what values -are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc). Three additional kinds of keywords can -also be specified (c_ID, f_ID, v_name), where a compute -or fix or variable provides the value to be -output. In each case, the compute, fix, or variable must generate -global values for input to the thermo_style custom -command. -

    -

    Note that thermodynamic output values can be "extensive" or -"intensive". The former scale with the number of atoms in the system -(e.g. total energy), the latter do not (e.g. temperature). The -setting for thermo_modify norm determines whether -extensive quantities are normalized or not. Computes and fixes -produce either extensive or intensive values; see their individual doc -pages for details. Equal-style variables produce only -intensive values; you can include a division by "natoms" in the -formula if desired, to make an extensive calculation produce an -intensive result. -

    -
    Dump file output -
    -

    Dump file output is specified by the dump and -dump_modify commands. There are several -pre-defined formats (dump atom, dump xtc, etc). -

    -

    There is also a dump custom format where the user -specifies what values are output with each atom. Pre-defined atom -attributes can be specified (id, x, fx, etc). Three additional kinds -of keywords can also be specified (c_ID, f_ID, v_name), where a -compute or fix or variable -provides the values to be output. In each case, the compute, fix, or -variable must generate per-atom values for input to the dump -custom command. -

    -

    There is also a dump local format where the user specifies -what local values to output. A pre-defined index keyword can be -specified to enumuerate the local values. Two additional kinds of -keywords can also be specified (c_ID, f_ID), where a -compute or fix or variable -provides the values to be output. In each case, the compute or fix -must generate local values for input to the dump local -command. -

    -
    Fixes that write output files -
    -

    Several fixes take various quantities as input and can write output -files: fix ave/time, fix -ave/spatial, fix ave/histo, -fix ave/correlate, and fix -print. -

    -

    The fix ave/time command enables direct output to -a file and/or time-averaging of global scalars or vectors. The user -specifies one or more quantities as input. These can be global -compute values, global fix values, or -variables of any style except the atom style which -produces per-atom values. Since a variable can refer to keywords used -by the thermo_style custom command (like temp or -press) and individual per-atom values, a wide variety of quantities -can be time averaged and/or output in this way. If the inputs are one -or more scalar values, then the fix generate a global scalar or vector -of output. If the inputs are one or more vector values, then the fix -generates a global vector or array of output. The time-averaged -output of this fix can also be used as input to other output commands. -

    -

    The fix ave/spatial command enables direct -output to a file of spatial-averaged per-atom quantities like those -output in dump files, within 1d layers of the simulation box. The -per-atom quantities can be atom density (mass or number) or atom -attributes such as position, velocity, force. They can also be -per-atom quantities calculated by a compute, by a -fix, or by an atom-style variable. The -spatial-averaged output of this fix can also be used as input to other -output commands. -

    -

    The fix ave/histo command enables direct output -to a file of histogrammed quantities, which can be global or per-atom -or local quantities. The histogram output of this fix can also be -used as input to other output commands. -

    -

    The fix ave/correlate command enables direct -output to a file of time-correlated quantities, which can be global -scalars. The correlation matrix output of this fix can also be used -as input to other output commands. -

    -

    The fix print command can generate a line of output -written to the screen and log file or to a separate file, periodically -during a running simulation. The line can contain one or more -variable values for any style variable except the atom -style). As explained above, variables themselves can contain -references to global values generated by thermodynamic -keywords, computes, -fixes, or other variables, or to per-atom -values for a specific atom. Thus the fix print -command is a means to output a wide variety of quantities separate -from normal thermodynamic or dump file output. -

    -
    Computes that process output quantities -
    -

    The compute reduce and compute -reduce/region commands take one or more per-atom -or local vector quantities as inputs and "reduce" them (sum, min, max, -ave) to scalar quantities. These are produced as output values which -can be used as input to other output commands. -

    -

    The compute slice command take one or more global -vector or array quantities as inputs and extracts a subset of their -values to create a new vector or array. These are produced as output -values which can be used as input to other output commands. -

    -

    The compute property/atom command takes a -list of one or more pre-defined atom attributes (id, x, fx, etc) and -stores the values in a per-atom vector or array. These are produced -as output values which can be used as input to other output commands. -The list of atom attributes is the same as for the dump -custom command. -

    -

    The compute property/local command takes -a list of one or more pre-defined local attributes (bond info, angle -info, etc) and stores the values in a local vector or array. These -are produced as output values which can be used as input to other -output commands. -

    -
    Fixes that process output quantities -
    -

    The fix vector command can create global vectors as -output from global scalars as input, accumulating them one element at -a time. -

    -

    The fix ave/atom command performs time-averaging -of per-atom vectors. The per-atom quantities can be atom attributes -such as position, velocity, force. They can also be per-atom -quantities calculated by a compute, by a -fix, or by an atom-style variable. The -time-averaged per-atom output of this fix can be used as input to -other output commands. -

    -

    The fix store/state command can archive one or -more per-atom attributes at a particular time, so that the old values -can be used in a future calculation or output. The list of atom -attributes is the same as for the dump custom command, -including per-atom quantities calculated by a compute, -by a fix, or by an atom-style variable. -The output of this fix can be used as input to other output commands. -

    -
    Computes that generate values to output -
    -

    Every compute in LAMMPS produces either global or -per-atom or local values. The values can be scalars or vectors or -arrays of data. These values can be output using the other commands -described in this section. The doc page for each compute command -describes what it produces. Computes that produce per-atom or local -values have the word "atom" or "local" in their style name. Computes -without the word "atom" or "local" produce global values. -

    -
    Fixes that generate values to output -
    -

    Some fixes in LAMMPS produces either global or per-atom or -local values which can be accessed by other commands. The values can -be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The doc page for -each fix command tells whether it produces any output quantities and -describes them. -

    -
    Variables that generate values to output -
    -

    Every variables defined in an input script generates -either a global scalar value or a per-atom vector (only atom-style -variables) when it is accessed. The formulas used to define equal- -and atom-style variables can contain references to the thermodynamic -keywords and to global and per-atom data generated by computes, fixes, -and other variables. The values generated by variables can be output -using the other commands described in this section. -

    -
    Summary table of output options and data flow between commands -
    -

    This table summarizes the various commands that can be used for -generating output from LAMMPS. Each command produces output data of -some kind and/or writes data to a file. Most of the commands can take -data from other commands as input. Thus you can link many of these -commands together in pipeline form, where data produced by one command -is used as input to another command and eventually written to the -screen or to a file. Note that to hook two commands together the -output and input data types must match, e.g. global/per-atom/local -data and scalar/vector/array data. -

    -

    Also note that, as described above, when a command takes a scalar as -input, that could be an element of a vector or array. Likewise a -vector input could be a column of an array. -

    -
    - - - - - - - - - - - - - - - - - - - - -
    Command Input Output
    thermo_style custom global scalars screen, log file
    dump custom per-atom vectors dump file
    dump local local vectors dump file
    fix print global scalar from variable screen, file
    print global scalar from variable screen
    computes N/A global/per-atom/local scalar/vector/array
    fixes N/A global/per-atom/local scalar/vector/array
    variables global scalars, per-atom vectors global scalar, per-atom vector
    compute reduce per-atom/local vectors global scalar/vector
    compute slice global vectors/arrays global vector/array
    compute property/atom per-atom vectors per-atom vector/array
    compute property/local local vectors local vector/array
    fix vector global scalars global vector
    fix ave/atom per-atom vectors per-atom vector/array
    fix ave/time global scalars/vectors global scalar/vector/array, file
    fix ave/spatial per-atom vectors global array, file
    fix ave/histo global/per-atom/local scalars and vectors global array, file
    fix ave/correlate global scalars global array, file
    fix store/state per-atom vectors per-atom vector/array
    -
    - -
    - -

    6.16 Thermostatting, barostatting, and computing temperature -

    -

    Thermostatting means controlling the temperature of particles in an MD -simulation. Barostatting means controlling the pressure. Since the -pressure includes a kinetic component due to particle velocities, both -these operations require calculation of the temperature. Typically a -target temperature (T) and/or pressure (P) is specified by the user, -and the thermostat or barostat attempts to equilibrate the system to -the requested T and/or P. -

    -

    Temperature is computed as kinetic energy divided by some number of -degrees of freedom (and the Boltzmann constant). Since kinetic energy -is a function of particle velocity, there is often a need to -distinguish between a particle's advection velocity (due to some -aggregate motiion of particles) and its thermal velocity. The sum of -the two is the particle's total velocity, but the latter is often what -is wanted to compute a temperature. -

    -

    LAMMPS has several options for computing temperatures, any of which -can be used in thermostatting and barostatting. These compute -commands calculate temperature, and the compute -pressure command calculates pressure. -

    - -

    All but the first 3 calculate velocity biases directly (e.g. advection -velocities) that are removed when computing the thermal temperature. -Compute temp/sphere and compute -temp/asphere compute kinetic energy for -finite-size particles that includes rotational degrees of freedom. -They both allow for velocity biases indirectly, via an optional extra -argument, another temperature compute that subtracts a velocity bias. -This allows the translational velocity of spherical or aspherical -particles to be adjusted in prescribed ways. -

    -

    Thermostatting in LAMMPS is performed by fixes, or in one -case by a pair style. Several thermostatting fixes are available: -Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling -(temp/rescale). Dissipative particle dynamics (DPD) thermostatting -can be invoked via the dpd/tstat pair style: -

    - -

    Fix nvt only thermostats the translational velocity of -particles. Fix nvt/sllod also does this, except -that it subtracts out a velocity bias due to a deforming box and -integrates the SLLOD equations of motion. See the NEMD -simulations section of this page for further details. Fix -nvt/sphere and fix -nvt/asphere thermostat not only translation -velocities but also rotational velocities for spherical and aspherical -particles. -

    -

    DPD thermostatting alters pairwise interactions in a manner analagous -to the per-particle thermostatting of fix -langevin. -

    -

    Any of the thermostatting fixes can use temperature computes that -remove bias which has two effects. First, the current calculated -temperature, which is compared to the requested target temperature, is -caluclated with the velocity bias removed. Second, the thermostat -adjusts only the thermal temperature component of the particle's -velocities, which are the velocities with the bias removed. The -removed bias is then added back to the adjusted velocities. See the -doc pages for the individual fixes and for the -fix_modify command for instructions on how to assign -a temperature compute to a thermostatting fix. For example, you can -apply a thermostat to only the x and z components of velocity by using -it in conjunction with compute -temp/partial. Of you could thermostat only -the thermal temperature of a streaming flow of particles without -affecting the streaming velocity, by using compute -temp/profile. -

    -

    IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning -they update the velocities and positions of particles due to forces -and velocities respectively. The other thermostat fixes only adjust -velocities; they do NOT perform time integration updates. Thus they -should be used in conjunction with a constant NVE integration fix such -as these: -

    - -

    Barostatting in LAMMPS is also performed by fixes. Two -barosttating methods are currently available: Nose-Hoover (npt and -nph) and Berendsen: -

    - -

    The fix npt commands include a Nose-Hoover thermostat -and barostat. Fix nph is just a Nose/Hoover barostat; -it does no thermostatting. Both fix nph and fix -press/bernendsen can be used in conjunction -with any of the thermostatting fixes. -

    -

    As with the thermostats, fix npt and fix -nph only use translational motion of the particles in -computing T and P and performing thermo/barostatting. Fix -npt/sphere and fix -npt/asphere thermo/barostat using not only -translation velocities but also rotational velocities for spherical -and aspherical particles. -

    -

    All of the barostatting fixes use the compute -pressure compute to calculate a current -pressure. By default, this compute is created with a simple compute -temp (see the last argument of the compute -pressure command), which is used to calculated -the kinetic componenet of the pressure. The barostatting fixes can -also use temperature computes that remove bias for the purpose of -computing the kinetic componenet which contributes to the current -pressure. See the doc pages for the individual fixes and for the -fix_modify command for instructions on how to assign -a temperature or pressure compute to a barostatting fix. -

    -

    IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (fix -npt and fix nph) perform time -integration. Fix press/berendsen does NOT, -so it should be used with one of the constant NVE fixes or with one of -the NVT fixes. -

    -

    Finally, thermodynamic output, which can be setup via the -thermo_style command, often includes temperature -and pressure values. As explained on the doc page for the -thermo_style command, the default T and P are -setup by the thermo command itself. They are NOT the ones associated -with any thermostatting or barostatting fix you have defined or with -any compute that calculates a temperature or pressure. Thus if you -want to view these values of T and P, you need to specify them -explicitly via a thermo_style custom command. Or -you can use the thermo_modify command to -re-define what temperature or pressure compute is used for default -thermodynamic output. -

    -
    - -

    6.17 Walls -

    -

    Walls in an MD simulation are typically used to bound particle motion, -i.e. to serve as a boundary condition. -

    -

    Walls in LAMMPS can be of rough (made of particles) or idealized -surfaces. Ideal walls can be smooth, generating forces only in the -normal direction, or frictional, generating forces also in the -tangential direction. -

    -

    Rough walls, built of particles, can be created in various ways. The -particles themselves can be generated like any other particle, via the -lattice and create_atoms commands, -or read in via the read_data command. -

    -

    Their motion can be constrained by many different commands, so that -they do not move at all, move together as a group at constant velocity -or in response to a net force acting on them, move in a prescribed -fashion (e.g. rotate around a point), etc. Note that if a time -integration fix like fix nve or fix nvt -is not used with the group that contains wall particles, their -positions and velocities will not be updated. -

    -
    • fix aveforce - set force on particles to average value, so they move together -
    • fix setforce - set force on particles to a value, e.g. 0.0 -
    • fix freeze - freeze particles for use as granular walls -
    • fix nve/noforce - advect particles by their velocity, but without force -
    • fix move - prescribe motion of particles by a linear velocity, oscillation, rotation, variable -
    -

    The fix move command offers the most generality, since -the motion of individual particles can be specified with -variable formula which depends on time and/or the -particle position. -

    -

    For rough walls, it may be useful to turn off pairwise interactions -between wall particles via the neigh_modify -exclude command. -

    -

    Rough walls can also be created by specifying frozen particles that do -not move and do not interact with mobile particles, and then tethering -other particles to the fixed particles, via a bond. -The bonded particles do interact with other mobile particles. -

    -

    Idealized walls can be specified via several fix commands. Fix -wall/gran creates frictional walls for use with -granular particles; all the other commands create smooth walls. -

    - -

    The lj93, lj126, colloid, and harmonic styles all allow the -flat walls to move with a constant velocity, or oscillate in time. -The fix wall/region command offers the most -generality, since the region surface is treated as a wall, and the -geometry of the region can be a simple primitive volume (e.g. a -sphere, or cube, or plane), or a complex volume made from the union -and intersection of primitive volumes. Regions can also -specify a volume "interior" or "exterior" to the specified primitive -shape or union or intersection. Regions can also be -"dynamic" meaning they move with constant velocity, oscillate, or -rotate. -

    -

    The only frictional idealized walls currently in LAMMPS are flat or -curved surfaces specified by the fix wall/gran -command. At some point we plan to allow regoin surfaces to be used as -frictional walls, as well as triangulated surfaces. -

    -
    - -

    6.18 Elastic constants -

    -

    Elastic constants characterize the stiffness of a material. The formal -definition is provided by the linear relation that holds between the -stress and strain tensors in the limit of infinitesimal deformation. -In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where -the repeated indices imply summation. s_ij are the elements of the -symmetric stress tensor. e_kl are the elements of the symmetric strain -tensor. C_ijkl are the elements of the fourth rank tensor of elastic -constants. In three dimensions, this tensor has 3^4=81 elements. Using -Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij -is now the derivative of s_i w.r.t. e_j. Because s_i is itself a -derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at -most 7*6/2 = 21 distinct elements. -

    -

    At zero temperature, it is easy to estimate these derivatives by -deforming the simulation box in one of the six directions using the -change_box command and measuring the change in the -stress tensor. A general-purpose script that does this is given in the -examples/elastic directory described in this -section. -

    -

    Calculating elastic constants at finite temperature is more -challenging, because it is necessary to run a simulation that perfoms -time averages of differential properties. One way to do this is to -measure the change in average stress tensor in an NVT simulations when -the cell volume undergoes a finite deformation. In order to balance -the systematic and statistical errors in this method, the magnitude of -the deformation must be chosen judiciously, and care must be taken to -fully equilibrate the deformed cell before sampling the stress -tensor. Another approach is to sample the triclinic cell fluctuations -that occur in an NPT simulation. This method can also be slow to -converge and requires careful post-processing (Shinoda) -

    -
    - -

    6.19 Library interface to LAMMPS -

    -

    As described in Section_start 5, LAMMPS -can be built as a library, so that it can be called by another code, -used in a coupled manner with other -codes, or driven through a Python interface. -

    -

    All of these methodologies use a C-style interface to LAMMPS that is -provided in the files src/library.cpp and src/library.h. The -functions therein have a C-style argument list, but contain C++ code -you could write yourself in a C++ application that was invoking LAMMPS -directly. The C++ code in the functions illustrates how to invoke -internal LAMMPS operations. Note that LAMMPS classes are defined -within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ -application. -

    -

    Library.cpp contains these 5 basic functions: -

    -
    void lammps_open(int, char **, MPI_Comm, void **)
-void lammps_close(void *)
-int lammps_version(void *)
-void lammps_file(void *, char *)
-char *lammps_command(void *, char *) 
-
    -

    The lammps_open() function is used to initialize LAMMPS, passing in a -list of strings as if they were command-line -arguments when LAMMPS is run in -stand-alone mode from the command line, and a MPI communicator for -LAMMPS to run under. It returns a ptr to the LAMMPS object that is -created, and which is used in subsequent library calls. The -lammps_open() function can be called multiple times, to create -multiple instances of LAMMPS. -

    -

    LAMMPS will run on the set of processors in the communicator. This -means the calling code can run LAMMPS on all or a subset of -processors. For example, a wrapper script might decide to alternate -between LAMMPS and another code, allowing them both to run on all the -processors. Or it might allocate half the processors to LAMMPS and -half to the other code and run both codes simultaneously before -syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. -

    -

    The lammps_close() function is used to shut down an instance of LAMMPS -and free all its memory. -

    -

    The lammps_version() function can be used to determined the specific -version of the underlying LAMMPS code. This is particularly useful -when loading LAMMPS as a shared library via dlopen(). The code using -the library interface can than use this information to adapt to -changes to the LAMMPS command syntax between versions. The returned -LAMMPS version code is an integer (e.g. 2 Sep 2015 results in -20150902) that grows with every new LAMMPS version. -

    -

    The lammps_file() and lammps_command() functions are used to pass a -file or string to LAMMPS as if it were an input script or single -command in an input script. Thus the calling code can read or -generate a series of LAMMPS commands one line at a time and pass it -thru the library interface to setup a problem and then run it, -interleaving the lammps_command() calls with other calls to extract -information from LAMMPS, perform its own operations, or call another -code's library. -

    -

    Other useful functions are also included in library.cpp. For example: -

    -
    void *lammps_extract_global(void *, char *)
-void *lammps_extract_atom(void *, char *)
-void *lammps_extract_compute(void *, char *, int, int)
-void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *)
-int lammps_set_variable(void *, char *, char *)
-int lammps_get_natoms(void *)
-void lammps_get_coords(void *, double *)
-void lammps_put_coords(void *, double *) 
-
    -

    These can extract various global or per-atom quantities from LAMMPS as -well as values calculated by a compute, fix, or variable. The -"set_variable" function can set an existing string-style variable to a -new value, so that subsequent LAMMPS commands can access the variable. -The "get" and "put" operations can retrieve and reset atom -coordinates. See the library.cpp file and its associated header file -library.h for details. -

    -

    The key idea of the library interface is that you can write any -functions you wish to define how your code talks to LAMMPS and add -them to src/library.cpp and src/library.h, as well as to the Python -interface. The routines you add can access or -change any LAMMPS data you wish. The examples/COUPLE and python -directories have example C++ and C and Python codes which show how a -driver code can link to LAMMPS as a library, run LAMMPS on a subset of -processors, grab data from LAMMPS, change it, and put it back into -LAMMPS. -

    -
    - -

    6.20 Calculating thermal conductivity -

    -

    The thermal conductivity kappa of a material can be measured in at -least 4 ways using various options in LAMMPS. See the examples/KAPPA -directory for scripts that implement the 4 methods discussed here for -a simple Lennard-Jones fluid model. Also, see this -section of the manual for an analogous -discussion for viscosity. -

    -

    The thermal conducitivity tensor kappa is a measure of the propensity -of a material to transmit heat energy in a diffusive manner as given -by Fourier's law -

    -

    J = -kappa grad(T) -

    -

    where J is the heat flux in units of energy per area per time and -grad(T) is the spatial gradient of temperature. The thermal -conductivity thus has units of energy per distance per time per degree -K and is often approximated as an isotropic quantity, i.e. as a -scalar. -

    -

    The first method is to setup two thermostatted regions at opposite -ends of a simulation box, or one in the middle and one at the end of a -periodic box. By holding the two regions at different temperatures -with a thermostatting fix, the energy -added to the hot region should equal the energy subtracted from the -cold region and be proportional to the heat flux moving between the -regions. See the paper by Ikeshoji and Hafskjold for -details of this idea. Note that thermostatting fixes such as fix -nvt, fix langevin, and fix -temp/rescale store the cumulative energy they -add/subtract. -

    -

    Alternatively, as a second method, the fix heat -command can used in place of thermostats on each of two regions to -add/subtract specified amounts of energy to both regions. In both -cases, the resulting temperatures of the two regions can be monitored -with the "compute temp/region" command and the temperature profile of -the intermediate region can be monitored with the fix -ave/spatial and compute -ke/atom commands. -

    -

    The third method is to perform a reverse non-equilibrium MD simulation -using the fix thermal/conductivity -command which implements the rNEMD algorithm of Muller-Plathe. -Kinetic energy is swapped between atoms in two different layers of the -simulation box. This induces a temperature gradient between the two -layers which can be monitored with the fix -ave/spatial and compute -ke/atom commands. The fix tallies the -cumulative energy transfer that it performs. See the fix -thermal/conductivity command for -details. -

    -

    The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the heat flux -to kappa. The heat flux can be calculated from the fluctuations of -per-atom potential and kinetic energies and per-atom stress tensor in -a steady-state equilibrated simulation. This is in contrast to the -two preceding non-equilibrium methods, where energy flows continuously -between hot and cold regions of the simulation box. -

    -

    The compute heat/flux command can calculate -the needed heat flux and describes how to implement the Green_Kubo -formalism using additional LAMMPS commands, such as the fix -ave/correlate command to calculate the needed -auto-correlation. See the doc page for the compute -heat/flux command for an example input script -that calculates the thermal conductivity of solid Ar via the GK -formalism. -

    -
    - -

    6.21 Calculating viscosity -

    -

    The shear viscosity eta of a fluid can be measured in at least 4 ways -using various options in LAMMPS. See the examples/VISCOSITY directory -for scripts that implement the 4 methods discussed here for a simple -Lennard-Jones fluid model. Also, see this -section of the manual for an analogous -discussion for thermal conductivity. -

    -

    Eta is a measure of the propensity of a fluid to transmit momentum in -a direction perpendicular to the direction of velocity or momentum -flow. Alternatively it is the resistance the fluid has to being -sheared. It is given by -

    -

    J = -eta grad(Vstream) -

    -

    where J is the momentum flux in units of momentum per area per time. -and grad(Vstream) is the spatial gradient of the velocity of the fluid -moving in another direction, normal to the area through which the -momentum flows. Viscosity thus has units of pressure-time. -

    -

    The first method is to perform a non-equlibrium MD (NEMD) simulation -by shearing the simulation box via the fix deform -command, and using the fix nvt/sllod command to -thermostat the fluid via the SLLOD equations of motion. -Alternatively, as a second method, one or more moving walls can be -used to shear the fluid in between them, again with some kind of -thermostat that modifies only the thermal (non-shearing) components of -velocity to prevent the fluid from heating up. -

    -

    In both cases, the velocity profile setup in the fluid by this -procedure can be monitored by the fix -ave/spatial command, which determines -grad(Vstream) in the equation above. E.g. the derivative in the -y-direction of the Vx component of fluid motion or grad(Vstream) = -dVx/dy. The Pxy off-diagonal component of the pressure or stress -tensor, as calculated by the compute pressure -command, can also be monitored, which is the J term in the equation -above. See this section of the manual -for details on NEMD simulations. -

    -

    The third method is to perform a reverse non-equilibrium MD simulation -using the fix viscosity command which implements -the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is -swapped between atoms in two different layers of the simulation box in -a different dimension. This induces a velocity gradient which can be -monitored with the fix ave/spatial command. -The fix tallies the cummulative momentum transfer that it performs. -See the fix viscosity command for details. -

    -

    The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the -stress/pressure tensor to eta. This can be done in a steady-state -equilibrated simulation which is in contrast to the two preceding -non-equilibrium methods, where momentum flows continuously through the -simulation box. -

    -

    Here is an example input script that calculates the viscosity of -liquid Ar via the GK formalism: -

    -
    # Sample LAMMPS input script for viscosity of liquid Ar 
-
    -
    units       real
-variable    T equal 86.4956
-variable    V equal vol
-variable    dt equal 4.0
-variable    p equal 400     # correlation length
-variable    s equal 5       # sample interval
-variable    d equal $p*$s   # dump interval 
-
    -
    # convert from LAMMPS real units to SI 
-
    -
    variable    kB equal 1.3806504e-23    # [J/K/ Boltzmann
-variable    atm2Pa equal 101325.0
-variable    A2m equal 1.0e-10
-variable    fs2s equal 1.0e-15
-variable    convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m} 
-
    -
    # setup problem 
-
    -
    dimension    3
-boundary     p p p
-lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
-region       box block 0 4 0 4 0 4
-create_box   1 box
-create_atoms 1 box
-mass	     1 39.948
-pair_style   lj/cut 13.0
-pair_coeff   * * 0.2381 3.405
-timestep     ${dt}
-thermo	     $d 
-
    -
    # equilibration and thermalization 
-
    -
    velocity     all create $T 102486 mom yes rot yes dist gaussian
-fix          NVT all nvt temp $T $T 10 drag 0.2
-run          8000 
-
    -
    # viscosity calculation, switch to NVE if desired 
-
    -
    #unfix       NVT
-#fix         NVE all nve 
-
    -
    reset_timestep 0
-variable     pxy equal pxy
-variable     pxz equal pxz
-variable     pyz equal pyz
-fix          SS all ave/correlate $s $p $d &
-             v_pxy v_pxz v_pyz type auto file S0St.dat ave running
-variable     scale equal ${convert}/(${kB}*$T)*$V*$s*${dt}
-variable     v11 equal trap(f_SS[3])*${scale}
-variable     v22 equal trap(f_SS[4])*${scale}
-variable     v33 equal trap(f_SS[5])*${scale}
-thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
-run          100000
-variable     v equal (v_v11+v_v22+v_v33)/3.0
-variable     ndens equal count(all)/vol
-print        "average viscosity: $v [Pa.s/ @ $T K, ${ndens} /A^3" 
-
    -
    - -

    6.22 Calculating a diffusion coefficient -

    -

    The diffusion coefficient D of a material can be measured in at least -2 ways using various options in LAMMPS. See the examples/DIFFUSE -directory for scripts that implement the 2 methods discussed here for -a simple Lennard-Jones fluid model. -

    -

    The first method is to measure the mean-squared displacement (MSD) of -the system, via the compute msd command. The slope -of the MSD versus time is proportional to the diffusion coefficient. -The instantaneous MSD values can be accumulated in a vector via the -fix vector command, and a line fit to the vector to -compute its slope via the variable slope function, and -thus extract D. -

    -

    The second method is to measure the velocity auto-correlation function -(VACF) of the system, via the compute vacf -command. The time-integral of the VACF is proportional to the -diffusion coefficient. The instantaneous VACF values can be -accumulated in a vector via the fix vector command, -and time integrated via the variable trap function, -and thus extract D. -

    -
    - -

    6.23 Using chunks to calculate system properties -

    -

    In LAMMS, "chunks" are collections of atoms, as defined by the -compute chunk/atom command, which assigns -each atom to a chunk ID (or to no chunk at all). The number of chunks -and the assignment of chunk IDs to atoms can be static or change over -time. Examples of "chunks" are molecules or spatial bins or atoms -with similar values (e.g. coordination number or potential energy). -

    -

    The per-atom chunk IDs can be used as input to two other kinds of -commands, to calculate various properties of a system: -

    - -

    Here, each of the 3 kinds of chunk-related commands is briefly -overviewed. Then some examples are given of how to compute different -properties with chunk commands. -

    -
    Compute chunk/atom command: -
    -

    This compute can assign atoms to chunks of various styles. Only atoms -in the specified group and optional specified region are assigned to a -chunk. Here are some possible chunk definitions: -

    -
    - - - - - - - -
    atoms in same molecule chunk ID = molecule ID
    atoms of same atom type chunk ID = atom type
    all atoms with same atom property (charge, radius, etc) chunk ID = output of compute property/atom
    atoms in same cluster chunk ID = output of compute cluster/atom command
    atoms in same spatial bin chunk ID = bin ID
    atoms in same rigid body chunk ID = molecule ID used to define rigid bodies
    atoms with similar potential energy chunk ID = output of compute pe/atom
    atoms with same local defect structure chunk ID = output of compute centro/atom or compute coord/atom command -
    - -

    Note that chunk IDs are integer values, so for atom properties or -computes that produce a floating point value, they will be truncated -to an integer. You could also use the compute in a variable that -scales the floating point value to spread it across multiple intergers. -

    -

    Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = -pencils, 3d bins = boxes, spherical bins, cylindrical bins. -

    -

    This compute also calculates the number of chunks Nchunk, which is -used by other commands to tally per-chunk data. Nchunk can be a -static value or change over time (e.g. the number of clusters). The -chunk ID for an individual atom can also be static (e.g. a molecule -ID), or dynamic (e.g. what spatial bin an atom is in as it moves). -

    -

    Note that this compute allows the per-atom output of other -computes, fixes, and -variables to be used to define chunk IDs for each -atom. This means you can write your own compute or fix to output a -per-atom quantity to use as chunk ID. See -Section_modify of the documentation for how to -do this. You can also define a per-atom variable in -the input script that uses a formula to generate a chunk ID for each -atom. -

    -
    Fix ave/chunk command: -
    -

    This fix takes the ID of a compute -chunk/atom command as input. For each chunk, -it then sums one or more specified per-atom values over the atoms in -each chunk. The per-atom values can be any atom property, such as -velocity, force, charge, potential energy, kinetic energy, stress, -etc. Additional keywords are defined for per-chunk properties like -density and temperature. More generally any per-atom value generated -by other computes, fixes, and per-atom -variables, can be summed over atoms in each chunk. -

    -

    Similar to other averaging fixes, this fix allows the summed per-chunk -values to be time-averaged in various ways, and output to a file. The -fix produces a global array as output with one row of values per -chunk. -

    -
    Compute */chunk commands: -
    -

    Currently the following computes operate on chunks of atoms to produce -per-chunk values. -

    - -

    They each take the ID of a compute -chunk/atom command as input. As their names -indicate, they calculate the center-of-mass, radius of gyration, -moments of inertia, mean-squared displacement, temperature, torque, -and velocity of center-of-mass for each chunk of atoms. The compute -property/chunk command can tally the -count of atoms in each chunk and extract other per-chunk properties. -

    -

    The reason these various calculations are not part of the fix -ave/chunk command, is that each requires a more -complicated operation than simply summing and averaging over per-atom -values in each chunk. For example, many of them require calculation -of a center of mass, which requires summing mass*position over the -atoms and then dividing by summed mass. -

    -

    All of these computes produce a global vector or global array as -output, wih one or more values per chunk. They can be used -in various ways: -

    -
    • As input to the fix ave/time command, which can -write the values to a file and optionally time average them. - -
    • As input to the fix ave/histo command to -histogram values across chunks. E.g. a histogram of cluster sizes or -molecule diffusion rates. - -
    • As input to special functions of equal-style -variables, like sum() and max(). E.g. to find the -largest cluster or fastest diffusing molecule. -
    -
    Example calculations with chunks -
    -

    Here are eaxmples using chunk commands to calculate various -properties: -

    -

    (1) Average velocity in each of 1000 2d spatial bins: -

    -
    compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
-fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out 
-
    -

    (2) Temperature in each spatial bin, after subtracting a flow -velocity: -

    -
    compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
-compute vbias all temp/profile 1 0 0 y 10
-fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out 
-
    -

    (3) Center of mass of each molecule: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    (4) Total force on each molecule and ave/max across all molecules: -

    -
    compute cc1 all chunk/atom molecule
-fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
-variable xave equal ave(f_12)
-variable xmax equal max(f_12)
-thermo 1000
-thermo_style custom step temp v_xave v_xmax 
-
    -

    (5) Histogram of cluster sizes: -

    -
    compute cluster all cluster/atom 1.0
-compute cc1 all chunk/atom c_cluster compress yes
-compute size all property/chunk cc1 count
-fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo 
-
    -
    - -

    6.24 Setting parameters for the kspace_style pppm/disp command -

    -

    The PPPM method computes interactions by splitting the pair potential -into two parts, one of which is computed in a normal pairwise fashion, -the so-called real-space part, and one of which is computed using the -Fourier transform, the so called reciprocal-space or kspace part. For -both parts, the potential is not computed exactly but is approximated. -Thus, there is an error in both parts of the computation, the -real-space and the kspace error. The just mentioned facts are true -both for the PPPM for Coulomb as well as dispersion interactions. The -deciding difference - and also the reason why the parameters for -pppm/disp have to be selected with more care - is the impact of the -errors on the results: The kspace error of the PPPM for Coulomb and -dispersion interaction and the real-space error of the PPPM for -Coulomb interaction have the character of noise. In contrast, the -real-space error of the PPPM for dispersion has a clear physical -interpretation: the underprediction of cohesion. As a consequence, the -real-space error has a much stronger effect than the kspace error on -simulation results for pppm/disp. Parameters must thus be chosen in a -way that this error is much smaller than the kspace error. -

    -

    When using pppm/disp and not making any specifications on the PPPM -parameters via the kspace modify command, parameters will be tuned -such that the real-space error and the kspace error are equal. This -will result in simulations that are either inaccurate or slow, both of -which is not desirable. For selecting parameters for the pppm/disp -that provide fast and accurate simulations, there are two approaches, -which both have their up- and downsides. -

    -

    The first approach is to set desired real-space an kspace accuracies -via the kspace_modify force/disp/real and kspace_modify -force/disp/kspace commands. Note that the accuracies have to be -specified in force units and are thus dependend on the chosen unit -settings. For real units, 0.0001 and 0.002 seem to provide reasonable -accurate and efficient computations for the real-space and kspace -accuracies. 0.002 and 0.05 work well for most systems using lj -units. PPPM parameters will be generated based on the desired -accuracies. The upside of this approach is that it usually provides a -good set of parameters and will work for both the kspace_modify diff -ad and kspace_modify diff ik options. The downside of the method -is that setting the PPPM parameters will take some time during the -initialization of the simulation. -

    -

    The second approach is to set the parameters for the pppm/disp -explicitly using the kspace_modify mesh/disp, kspace_modify -order/disp, and kspace_modify gewald/disp commands. This approach -requires a more experienced user who understands well the impact of -the choice of parameters on the simulation accuracy and -performance. This approach provides a fast initialization of the -simulation. However, it is sensitive to errors: A combination of -parameters that will perform well for one system might result in -far-from-optimal conditions for other simulations. For example, -parametes that provide accurate and fast computations for -all-atomistic force fields can provide insufficient accuracy or -united-atomistic force fields (which is related to that the latter -typically have larger dispersion coefficients). -

    -

    To avoid inaccurate or inefficient simulations, the pppm/disp stops -simulations with an error message if no action is taken to control the -PPPM parameters. If the automatic parameter generation is desired and -real-space and kspace accuracies are desired to be equal, this error -message can be suppressed using the kspace_modify disp/auto yes -command. -

    -

    A reasonable approach that combines the upsides of both methods is to -make the first run using the kspace_modify force/disp/real and -kspace_modify force/disp/kspace commands, write down the PPPM -parameters from the outut, and specify these parameters using the -second approach in subsequent runs (which have the same composition, -force field, and approximately the same volume). -

    -

    Concerning the performance of the pppm/disp there are two more things -to consider. The first is that when using the pppm/disp, the cutoff -parameter does no longer affect the accuracy of the simulation -(subject to that gewald/disp is adjusted when changing the cutoff). -The performance can thus be increased by examining different values -for the cutoff parameter. A lower bound for the cutoff is only set by -the truncation error of the repulsive term of pair potentials. -

    -

    The second is that the mixing rule of the pair style has an impact on -the computation time when using the pppm/disp. Fastest computations -are achieved when using the geometric mixing rule. Using the -arithmetic mixing rule substantially increases the computational cost. -The computational overhead can be reduced using the kspace_modify -mix/disp geom and kspace_modify splittol commands. The first -command simply enforces geometric mixing of the dispersion -coeffiecients in kspace computations. This introduces some error in -the computations but will also significantly speed-up the -simulations. The second keyword sets the accuracy with which the -dispersion coefficients are approximated using a matrix factorization -approach. This may result in better accuracy then using the first -command, but will usually also not provide an equally good increase of -efficiency. -

    -

    Finally, pppm/disp can also be used when no mixing rules apply. -This can be achieved using the kspace_modify mix/disp none command. -Note that the code does not check automatically whether any mixing -rule is fulfilled. If mixing rules do not apply, the user will have -to specify this command explicitly. -

    -
    - -

    6.25 Polarizable models -

    -

    In polarizable force fields the charge distributions in molecules and -materials respond to their electrostatic environements. Polarizable -systems can be simulated in LAMMPS using three methods: -

    -
    • the fluctuating charge method, implemented in the QEQ -package, - -
    • the adiabatic core-shell method, implemented in the -CORESHELL package, - -
    • the thermalized Drude dipole method, implemented in the -USER-DRUDE package. -
    -

    The fluctuating charge method calculates instantaneous charges on -interacting atoms based on the electronegativity equalization -principle. It is implemented in the fix qeq which is -available in several variants. It is a relatively efficient technique -since no additional particles are introduced. This method allows for -charge transfer between molecules or atom groups. However, because the -charges are located at the interaction sites, off-plane components of -polarization cannot be represented in planar molecules or atom groups. -

    -

    The two other methods share the same basic idea: polarizable atoms are -split into one core atom and one satellite particle (called shell or -Drude particle) attached to it by a harmonic spring. Both atoms bear -a charge and they represent collectively an induced electric dipole. -These techniques are computationally more expensive than the QEq -method because of additional particles and bonds. These two -charge-on-spring methods differ in certain features, with the -core-shell model being normally used for ionic/crystalline materials, -whereas the so-called Drude model is normally used for molecular -systems and fluid states. -

    -

    The core-shell model is applicable to crystalline materials where the -high symmetry around each site leads to stable trajectories of the -core-shell pairs. However, bonded atoms in molecules can be so close -that a core would interact too strongly or even capture the Drude -particle of a neighbor. The Drude dipole model is relatively more -complex in order to remediate this and other issues. Specifically, the -Drude model includes specific thermostating of the core-Drude pairs -and short-range damping of the induced dipoles. -

    -

    The three polarization methods can be implemented through a -self-consistent calculation of charges or induced dipoles at each -timestep. In the fluctuating charge scheme this is done by the matrix -inversion method in fix qeq/point, but for core-shell -or Drude-dipoles the relaxed-dipoles technique would require an slow -iterative procedure. These self-consistent solutions yield accurate -trajectories since the additional degrees of freedom representing -polarization are massless. An alternative is to attribute a mass to -the additional degrees of freedom and perform time integration using -an extended Lagrangian technique. For the fluctuating charge scheme -this is done by fix qeq/dynamic, and for the -charge-on-spring models by the methods outlined in the next two -sections. The assignment of masses to the additional degrees of -freedom can lead to unphysical trajectories if care is not exerted in -choosing the parameters of the poarizable models and the simulation -conditions. -

    -

    In the core-shell model the vibration of the shells is kept faster -than the ionic vibrations to mimic the fast response of the -polarizable electrons. But in molecular systems thermalizing the -core-Drude pairs at temperatures comparable to the rest of the -simulation leads to several problems (kinetic energy transfer, too -short a timestep, etc.) In order to avoid these problems the relative -motion of the Drude particles with respect to their cores is kept -"cold" so the vibration of the core-Drude pairs is very slow, -approaching the self-consistent regime. In both models the -temperature is regulated using the velocities of the center of mass of -core+shell (or Drude) pairs, but in the Drude model the actual -relative core-Drude particle motion is thermostated separately as -well. -

    -
    - -

    6.26 Adiabatic core/shell model -

    -

    The adiabatic core-shell model by Mitchell and -Finchham is a simple method for adding -polarizability to a system. In order to mimic the electron shell of -an ion, a satellite particle is attached to it. This way the ions are -split into a core and a shell where the latter is meant to react to -the electrostatic environment inducing polarizability. -

    -

    Technically, shells are attached to the cores by a spring force f = -k*r where k is a parametrized spring constant and r is the distance -between the core and the shell. The charges of the core and the shell -add up to the ion charge, thus q(ion) = q(core) + q(shell). This -setup introduces the ion polarizability (alpha) given by -alpha = q(shell)^2 / k. In a -similar fashion the mass of the ion is distributed on the core and the -shell with the core having the larger mass. -

    -

    To run this model in LAMMPS, atom_style full can -be used since atom charge and bonds are needed. Each kind of -core/shell pair requires two atom types and a bond type. The core and -shell of a core/shell pair should be bonded to each other with a -harmonic bond that provides the spring force. For example, a data file -for NaCl, as found in examples/coreshell, has this format: -

    -
    432   atoms  # core and shell atoms
-216   bonds  # number of core/shell springs 
-
    -
    4     atom types  # 2 cores and 2 shells for Na and Cl 
-2     bond types 
-
    -
    0.0 24.09597 xlo xhi
-0.0 24.09597 ylo yhi
-0.0 24.09597 zlo zhi 
-
    -
    Masses       # core/shell mass ratio = 0.1 
-
    -
    1 20.690784  # Na core
-2 31.90500   # Cl core
-3 2.298976   # Na shell
-4 3.54500    # Cl shell 
-
    -
    Atoms 
-
    -
    1    1    2   1.5005    0.00000000   0.00000000   0.00000000 # core of core/shell pair 1
-2    1    4  -2.5005    0.00000000   0.00000000   0.00000000 # shell of core/shell pair 1
-3    2    1   1.5056    4.01599500   4.01599500   4.01599500 # core of core/shell pair 2
-4    2    3  -0.5056    4.01599500   4.01599500   4.01599500 # shell of core/shell pair 2 
-(...) 
-
    -
    Bonds   # Bond topology for spring forces 
-
    -
    1     2     1     2   # spring for core/shell pair 1
-2     2     3     4   # spring for core/shell pair 2 
-(...) 
-
    -

    Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only -defined between the shells. Coulombic interactions are defined -between all cores and shells. If desired, additional bonds can be -specified between cores. -

    -

    The special_bonds command should be used to -turn-off the Coulombic interaction within core/shell pairs, since that -interaction is set by the bond spring. This is done using the -special_bonds command with a 1-2 weight = 0.0, -which is the default value. It needs to be considered whether one has -to adjust the special_bonds weighting according -to the molecular topology since the interactions of the shells are -bypassed over an extra bond. -

    -

    Note that this core/shell implementation does not require all ions to -be polarized. One can mix core/shell pairs and ions without a -satellite particle if desired. -

    -

    Since the core/shell model permits distances of r = 0.0 between the -core and shell, a pair style with a "cs" suffix needs to be used to -implement a valid long-range Coulombic correction. Several such pair -styles are provided in the CORESHELL package. See this doc -page for details. All of the core/shell enabled pair -styles require the use of a long-range Coulombic solver, as specified -by the kspace_style command. Either the PPPM or -Ewald solvers can be used. -

    -

    For the NaCL example problem, these pair style and bond style settings -are used: -

    -
    pair_style      born/coul/long/cs 20.0 20.0
-pair_coeff      * *      0.0 1.000   0.00  0.00   0.00
-pair_coeff      3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
-pair_coeff      3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
-pair_coeff      4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl 
-
    -
    bond_style      harmonic
-bond_coeff      1 63.014 0.0
-bond_coeff      2 25.724 0.0 
-
    -

    When running dynamics with the adiabatic core/shell model, the -following issues should be considered. Since the relative motion of -the core and shell particles corresponds to the polarization, typical -thermostats can alter the polarization behaviour, meaning the shell -will not react freely to its electrostatic environment. This is -critical during the equilibration of the system. Therefore -it's typically desirable to decouple the relative motion of the -core/shell pair, which is an imaginary degree of freedom, from the -real physical system. To do that, the compute -temp/cs command can be used, in conjunction with -any of the thermostat fixes, such as fix nvt or fix -langevin. This compute uses the center-of-mass velocity -of the core/shell pairs to calculate a temperature, and insures that -velocity is what is rescaled for thermostatting purposes. This -compute also works for a system with both core/shell pairs and -non-polarized ions (ions without an attached satellite particle). The -compute temp/cs command requires input of two -groups, one for the core atoms, another for the shell atoms. -Non-polarized ions which might also be included in the treated system -should not be included into either of these groups, they are taken -into account by the group-ID (2nd argument) of the compute. The -groups can be defined using the group type command. -Note that to perform thermostatting using this definition of -temperature, the fix modify temp command should be -used to assign the compute to the thermostat fix. Likewise the -thermo_modify temp command can be used to make -this temperature be output for the overall system. -

    -

    For the NaCl example, this can be done as follows: -

    -
    group cores type 1 2
-group shells type 3 4
-compute CSequ all temp/cs cores shells
-fix thermoberendsen all temp/berendsen 1427 1427 0.4    # thermostat for the true physical system
-fix thermostatequ all nve                               # integrator as needed for the berendsen thermostat
-fix_modify thermoberendsen temp CSequ
-thermo_modify temp CSequ                                # output of center-of-mass derived temperature 
-
    -

    If compute temp/cs is used, the decoupled -relative motion of the core and the shell should in theory be -stable. However numerical fluctuation can introduce a small -momentum to the system, which is noticable over long trajectories. -Therefore it is recomendable to use the fix -momentum command in combination with compute -temp/cs when equilibrating the system to -prevent any drift. -

    -

    When intializing the velocities of a system with core/shell pairs, it -is also desirable to not introduce energy into the relative motion of -the core/shell particles, but only assign a center-of-mass velocity to -the pairs. This can be done by using the bias keyword of the -velocity create command and assigning the compute -temp/cs command to the temp keyword of the -velocity commmand, e.g. -

    -
    velocity all create 1427 134 bias yes temp CSequ
-velocity all scale 1427 temp CSequ 
-
    -

    It is important to note that the polarizability of the core/shell -pairs is based on their relative motion. Therefore the choice of -spring force and mass ratio need to ensure much faster relative motion -of the 2 atoms within the core/shell pair than their center-of-mass -velocity. This allow the shells to effectively react instantaneously -to the electrostatic environment. This fast movement also limits the -timestep size that can be used. -

    -

    The primary literature of the adiabatic core/shell model suggests that -the fast relative motion of the core/shell pairs only allows negligible -energy transfer to the environment. Therefore it is not intended to -decouple the core/shell degree of freedom from the physical system -during production runs. In other words, the compute -temp/cs command should not be used during -production runs and is only required during equilibration. This way one -is consistent with literature (based on the code packages DL_POLY or -GULP for instance). -

    -

    The mentioned energy transfer will typically lead to a a small drift -in total energy over time. This internal energy can be monitored -using the compute chunk/atom and compute -temp/chunk commands. The internal kinetic -energies of each core/shell pair can then be summed using the sum() -special function of the variable command. Or they can -be time/averaged and output using the fix ave/time -command. To use these commands, each core/shell pair must be defined -as a "chunk". If each core/shell pair is defined as its own molecule, -the molecule ID can be used to define the chunks. If cores are bonded -to each other to form larger molecules, the chunks can be identified -by the fix property/atom via assigning a -core/shell ID to each atom using a special field in the data file read -by the read_data command. This field can then be -accessed by the compute property/atom -command, to use as input to the compute -chunk/atom command to define the core/shell -pairs as chunks. -

    -

    For example, -

    -
    fix csinfo all property/atom i_CSID                       # property/atom command
-read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
-compute prop all property/atom i_CSID
-compute cs_chunk all chunk/atom c_prop
-compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
-fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector 
-
    -

    The additional section in the date file would be formatted like this: -

    -
    CS-Info         # header of additional section 
-
    -
    1   1           # column 1 = atom ID, column 2 = core/shell ID 
-2   1   
-3   2   
-4   2   
-5   3   
-6   3   
-7   4   
-8   4   
-(...) 
-
    -
    - -

    6.27 Drude induced dipoles -

    -

    The thermalized Drude model, similarly to the core-shell -model, representes induced dipoles by a pair of charges (the core atom -and the Drude particle) connected by a harmonic spring. The Drude -model has a number of features aimed at its use in molecular systems -(Lamoureux and Roux): -

    -
    • Thermostating of the additional degrees of freedom associated with the -induced dipoles at very low temperature, in terms of the reduced -coordinates of the Drude particles with respect to their cores. This -makes the trajectory close to that of relaxed induced dipoles. - -
    • Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle -pair represents a single (polarizable) atom, so the special screening -factors in a covalent structure should be the same for the core and -the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4 -special neighbor relations from their respective cores. - -
    • Stabilization of the interactions between induced dipoles. Drude -dipoles on covalently bonded atoms interact too strongly due to the -short distances, so an atom may capture the Drude particle of a -neighbor, or the induced dipoles within the same molecule may align -too much. To avoid this, damping at short range can be done by Thole -functions (for which there are physical grounds). This Thole damping -is applied to the point charges composing the induced dipole (the -charge of the Drude particle and the opposite charge on the core, not -to the total charge of the core atom). -
    -

    A detailed tutorial covering the usage of Drude induced dipoles in -LAMMPS is available here. -

    -

    As with the core-shell model, the cores and Drude particles should -appear in the data file as standard atoms. The same holds for the -springs between them, which are described by standard harmonic bonds. -The nature of the atoms (core, Drude particle or non-polarizable) is -specified via the fix drude command. The special -list of neighbors is automatically refactored to account for the -equivalence of core and Drude particles as regards special 1-2 to 1-4 -screening. It may be necessary to use the extra keyword of the -special_bonds command. If using fix -shake, make sure no Drude particle is in this fix -group. -

    -

    There are two ways to thermostat the Drude particles at a low -temperature: use either fix langevin/drude -for a Langevin thermostat, or fix -drude/transform/* for a Nose-Hoover -thermostat. The former requires use of the command comm_modify vel -yes. The latter requires two separate integration -fixes like nvt or npt. The correct temperatures of the reduced -degrees of freedom can be calculated using the compute -temp/drude. This requires also to use the -command comm_modify vel yes. -

    -

    Short-range damping of the induced dipole interactions can be achieved -using Thole functions through the the pair style -thole in pair_style hybrid/overlay -with a Coulomb pair style. It may be useful to use coul/long/cs or -similar from the CORESHELL package if the core and Drude particle come -too close, which can cause numerical issues. -

    -
    - -
    - - - -

    (Berendsen) Berendsen, Grigera, Straatsma, J Phys Chem, 91, -6269-6271 (1987). -

    - - -

    (Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). -

    - - -

    (Horn) Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon, -J Chem Phys, 120, 9665 (2004). -

    - - -

    (Ikeshoji) Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 -(1994). -

    - - -

    (MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). -

    - - -

    (Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). -

    - - -

    (Jorgensen) Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). -

    - - -

    (Price) Price and Brooks, J Chem Phys, 121, 10096 (2004). -

    - - -

    (Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). -

    - - -

    (Mitchell and Finchham) Mitchell, Finchham, J Phys Condensed Matter, -5, 1031-1038 (1993). -

    - - -

    (Lamoureux and Roux) G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) -

    - diff --git a/doc/doc2/Section_intro.html b/doc/doc2/Section_intro.html deleted file mode 100644 index 2f99ec66eb..0000000000 --- a/doc/doc2/Section_intro.html +++ /dev/null @@ -1,551 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
    - - - - - - -
    - -

    1. Introduction -

    -

    This section provides an overview of what LAMMPS can and can't do, -describes what it means for LAMMPS to be an open-source code, and -acknowledges the funding and people who have contributed to LAMMPS -over the years. -

    -1.1 What is LAMMPS
    -1.2 LAMMPS features
    -1.3 LAMMPS non-features
    -1.4 Open source distribution
    -1.5 Acknowledgments and citations
    - -
    - -
    - -

    1.1 What is LAMMPS -

    -

    LAMMPS is a classical molecular dynamics code that models an ensemble -of particles in a liquid, solid, or gaseous state. It can model -atomic, polymeric, biological, metallic, granular, and coarse-grained -systems using a variety of force fields and boundary conditions. -

    -

    For examples of LAMMPS simulations, see the Publications page of the -LAMMPS WWW Site. -

    -

    LAMMPS runs efficiently on single-processor desktop or laptop -machines, but is designed for parallel computers. It will run on any -parallel machine that compiles C++ and supports the MPI -message-passing library. This includes distributed- or shared-memory -parallel machines and Beowulf-style clusters. -

    - - -

    LAMMPS can model systems with only a few particles up to millions or -billions. See Section_perf for information on -LAMMPS performance and scalability, or the Benchmarks section of the -LAMMPS WWW Site. -

    -

    LAMMPS is a freely-available open-source code, distributed under the -terms of the GNU Public License, which means you can use or -modify the code however you wish. See this section for a -brief discussion of the open-source philosophy. -

    - - -

    LAMMPS is designed to be easy to modify or extend with new -capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See Section_modify -for more details. -

    -

    The current version of LAMMPS is written in C++. Earlier versions -were written in F77 and F90. See -Section_history for more information on -different versions. All versions can be downloaded from the LAMMPS -WWW Site. -

    -

    LAMMPS was originally developed under a US Department of Energy CRADA -(Cooperative Research and Development Agreement) between two DOE labs -and 3 companies. It is distributed by Sandia National Labs. -See this section for more information on LAMMPS funding and -individuals who have contributed to LAMMPS. -

    - - -

    In the most general sense, LAMMPS integrates Newton's equations of -motion for collections of atoms, molecules, or macroscopic particles -that interact via short- or long-range forces with a variety of -initial and/or boundary conditions. For computational efficiency -LAMMPS uses neighbor lists to keep track of nearby particles. The -lists are optimized for systems with particles that are repulsive at -short distances, so that the local density of particles never becomes -too large. On parallel machines, LAMMPS uses spatial-decomposition -techniques to partition the simulation domain into small 3d -sub-domains, one of which is assigned to each processor. Processors -communicate and store "ghost" atom information for atoms that border -their sub-domain. LAMMPS is most efficient (in a parallel sense) for -systems whose particles fill a 3d rectangular box with roughly uniform -density. Papers with technical details of the algorithms used in -LAMMPS are listed in this section. -

    -
    - -

    1.2 LAMMPS features -

    -

    This section highlights LAMMPS features, with pointers to specific -commands which give more details. If LAMMPS doesn't have your -favorite interatomic potential, boundary condition, or atom type, see -Section_modify, which describes how you can add -it to LAMMPS. -

    -
    General features -
    -
    • runs on a single processor or in parallel -
    • distributed-memory message-passing parallelism (MPI) -
    • spatial-decomposition of simulation domain for parallelism -
    • open-source distribution -
    • highly portable C++ -
    • optional libraries used: MPI and single-processor FFT -
    • GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features -
    • easy to extend with new features and functionality -
    • runs from an input script -
    • syntax for defining and using variables and formulas -
    • syntax for looping over runs and breaking out of loops -
    • run one or multiple simulations simultaneously (in parallel) from one script -
    • build as library, invoke LAMMPS thru library interface or provided Python wrapper -
    • couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both -
    -
    Particle and model types -
    -

    (atom style command) -

    -
    • atoms -
    • coarse-grained particles (e.g. bead-spring polymers) -
    • united-atom polymers or organic molecules -
    • all-atom polymers, organic molecules, proteins, DNA -
    • metals -
    • granular materials -
    • coarse-grained mesoscale models -
    • finite-size spherical and ellipsoidal particles -
    • finite-size line segment (2d) and triangle (3d) particles -
    • point dipole particles -
    • rigid collections of particles -
    • hybrid combinations of these -
    -
    Force fields -
    -

    (pair style, bond style, -angle style, dihedral style, -improper style, kspace style -commands) -

    -
    • pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated -
    • charged pairwise potentials: Coulombic, point-dipole -
    • manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic -
    • long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald) -
    • polarization models: QEq, core/shell model, Drude dipole model -
    • charge equilibration (QEq via dynamic, point, shielded, Slater methods) -
    • coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO -
    • mesoscopic potentials: granular, Peridynamics, SPH -
    • electron force field (eFF, AWPMD) -
    • bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable) -
    • angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS) -
    • dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS -
    • improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS) -
    • polymer potentials: all-atom, united-atom, bead-spring, breakable -
    • water potentials: TIP3P, TIP4P, SPC -
    • implicit solvent potentials: hydrodynamic lubrication, Debye -
    • force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options -
    • access to KIM archive of potentials via pair kim -
    • hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation -
    • overlaid potentials: superposition of multiple pair potentials -
    -
    Atom creation -
    -

    (read_data, lattice, -create_atoms, delete_atoms, -displace_atoms, replicate commands) -

    -
    • read in atom coords from files -
    • create atoms on one or more lattices (e.g. grain boundaries) -
    • delete geometric or logical groups of atoms (e.g. voids) -
    • replicate existing atoms multiple times -
    • displace atoms -
    -
    Ensembles, constraints, and boundary conditions -
    -

    (fix command) -

    -
    • 2d or 3d systems -
    • orthogonal or non-orthogonal (triclinic symmetry) simulation domains -
    • constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators -
    • thermostatting options for groups and geometric regions of atoms -
    • pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions -
    • simulation box deformation (tensile and shear) -
    • harmonic (umbrella) constraint forces -
    • rigid body constraints -
    • SHAKE bond and angle constraints -
    • Monte Carlo bond breaking, formation, swapping -
    • atom/molecule insertion and deletion -
    • walls of various kinds -
    • non-equilibrium molecular dynamics (NEMD) -
    • variety of additional boundary conditions and constraints -
    -
    Integrators -
    -

    (run, run_style, minimize commands) -

    -
    • velocity-Verlet integrator -
    • Brownian dynamics -
    • rigid body integration -
    • energy minimization via conjugate gradient or steepest descent relaxation -
    • rRESPA hierarchical timestepping -
    • rerun command for post-processing of dump files -
    -
    Diagnostics -
    -
    • see the various flavors of the fix and compute commands -
    -
    Output -
    -

    (dump, restart commands) -

    -
    • log file of thermodynamic info -
    • text dump files of atom coords, velocities, other per-atom quantities -
    • binary restart files -
    • parallel I/O of dump and restart files -
    • per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc) -
    • user-defined system-wide (log file) or per-atom (dump file) calculations -
    • spatial and time averaging of per-atom quantities -
    • time averaging of system-wide quantities -
    • atom snapshots in native, XYZ, XTC, DCD, CFG formats -
    -
    Multi-replica models -
    -

    nudged elastic band -parallel replica dynamics -temperature accelerated dynamics -parallel tempering -

    -
    Pre- and post-processing -
    -
    • Various pre- and post-processing serial tools are packaged -with LAMMPS; see these doc pages. - -
    • Our group has also written and released a separate toolkit called -Pizza.py which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in Python and is available for download from the -Pizza.py WWW site. -
    - - - - -
    Specialized features -
    -

    These are LAMMPS capabilities which you may not think of as typical -molecular dynamics options: -

    - -
    - -

    1.3 LAMMPS non-features -

    -

    LAMMPS is designed to efficiently compute Newton's equations of motion -for a system of interacting particles. Many of the tools needed to -pre- and post-process the data for such simulations are not included -in the LAMMPS kernel for several reasons: -

    -
    • the desire to keep LAMMPS simple -
    • they are not parallel operations -
    • other codes already do them -
    • limited development resources -
    -

    Specifically, LAMMPS itself does not: -

    -
    • run thru a GUI -
    • build molecular systems -
    • assign force-field coefficients automagically -
    • perform sophisticated analyses of your MD simulation -
    • visualize your MD simulation -
    • plot your output data -
    -

    A few tools for pre- and post-processing tasks are provided as part of -the LAMMPS package; they are described in this -section. However, many people use other codes or -write their own tools for these tasks. -

    -

    As noted above, our group has also written and released a separate -toolkit called Pizza.py which addresses some of the listed -bullets. It provides tools for doing setup, analysis, plotting, and -visualization for LAMMPS simulations. Pizza.py is written in -Python and is available for download from the Pizza.py WWW -site. -

    -

    LAMMPS requires as input a list of initial atom coordinates and types, -molecular topology information, and force-field coefficients assigned -to all atoms and bonds. LAMMPS will not build molecular systems and -assign force-field parameters for you. -

    -

    For atomic systems LAMMPS provides a create_atoms -command which places atoms on solid-state lattices (fcc, bcc, -user-defined, etc). Assigning small numbers of force field -coefficients can be done via the pair coeff, bond -coeff, angle coeff, etc commands. -For molecular systems or more complicated simulation geometries, users -typically use another code as a builder and convert its output to -LAMMPS input format, or write their own code to generate atom -coordinate and molecular topology for LAMMPS to read in. -

    -

    For complicated molecular systems (e.g. a protein), a multitude of -topology information and hundreds of force-field coefficients must -typically be specified. We suggest you use a program like -CHARMM or AMBER or other molecular builders to setup -such problems and dump its information to a file. You can then -reformat the file as LAMMPS input. Some of the tools in this -section can assist in this process. -

    -

    Similarly, LAMMPS creates output files in a simple format. Most users -post-process these files with their own analysis tools or re-format -them for input into other programs, including visualization packages. -If you are convinced you need to compute something on-the-fly as -LAMMPS runs, see Section_modify for a discussion -of how you can use the dump and compute and -fix commands to print out data of your choosing. Keep in -mind that complicated computations can slow down the molecular -dynamics timestepping, particularly if the computations are not -parallel, so it is often better to leave such analysis to -post-processing codes. -

    -

    A very simple (yet fast) visualizer is provided with the LAMMPS -package - see the xmovie tool in this -section. It creates xyz projection views of -atomic coordinates and animates them. We find it very useful for -debugging purposes. For high-quality visualization we recommend the -following packages: -

    - -

    Other features that LAMMPS does not yet (and may never) support are -discussed in Section_history. -

    -

    Finally, these are freely-available molecular dynamics codes, most of -them parallel, which may be well-suited to the problems you want to -model. They can also be used in conjunction with LAMMPS to perform -complementary modeling tasks. -

    - - - - - - - - - - - - - -

    CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for -modeling biological molecules. CHARMM and AMBER use -atom-decomposition (replicated-data) strategies for parallelism; NAMD -and NWCHEM use spatial-decomposition approaches, similar to LAMMPS. -Tinker is a serial code. DL_POLY includes potentials for a variety of -biological and non-biological materials; both a replicated-data and -spatial-decomposition version exist. -

    -
    - -

    1.4 Open source distribution -

    -

    LAMMPS comes with no warranty of any kind. As each source file states -in its header, it is a copyrighted code that is distributed free-of- -charge, under the terms of the GNU Public License (GPL). This -is often referred to as open-source distribution - see -www.gnu.org or www.opensource.org for more -details. The legal text of the GPL is in the LICENSE file that is -included in the LAMMPS distribution. -

    - - - - -

    Here is a summary of what the GPL means for LAMMPS users: -

    -

    (1) Anyone is free to use, modify, or extend LAMMPS in any way they -choose, including for commercial purposes. -

    -

    (2) If you distribute a modified version of LAMMPS, it must remain -open-source, meaning you distribute it under the terms of the GPL. -You should clearly annotate such a code as a derivative version of -LAMMPS. -

    -

    (3) If you release any code that includes LAMMPS source code, then it -must also be open-sourced, meaning you distribute it under the terms -of the GPL. -

    -

    (4) If you give LAMMPS files to someone else, the GPL LICENSE file and -source file headers (including the copyright and GPL notices) should -remain part of the code. -

    -

    In the spirit of an open-source code, these are various ways you can -contribute to making LAMMPS better. You can send email to the -developers on any of these -items. -

    -
    • Point prospective users to the LAMMPS WWW Site. Mention it in -talks or link to it from your WWW site. - -
    • If you find an error or omission in this manual or on the LAMMPS WWW -Site, or have a suggestion for something to clarify or include, -send an email to the -developers. - -
    • If you find a bug, Section_errors 2 -describes how to report it. - -
    • If you publish a paper using LAMMPS results, send the citation (and -any cool pictures or movies if you like) to add to the Publications, -Pictures, and Movies pages of the LAMMPS WWW Site, with links -and attributions back to you. - -
    • Create a new Makefile.machine that can be added to the src/MAKE -directory. - -
    • The tools sub-directory of the LAMMPS distribution has various -stand-alone codes for pre- and post-processing of LAMMPS data. More -details are given in Section_tools. If you write -a new tool that users will find useful, it can be added to the LAMMPS -distribution. - -
    • LAMMPS is designed to be easy to extend with new code for features -like potentials, boundary conditions, diagnostic computations, etc. -This section gives details. If you add a -feature of general interest, it can be added to the LAMMPS -distribution. - -
    • The Benchmark page of the LAMMPS WWW Site lists LAMMPS -performance on various platforms. The files needed to run the -benchmarks are part of the LAMMPS distribution. If your machine is -sufficiently different from those listed, your timing data can be -added to the page. - -
    • You can send feedback for the User Comments page of the LAMMPS WWW -Site. It might be added to the page. No promises. - -
    • Cash. Small denominations, unmarked bills preferred. Paper sack OK. -Leave on desk. VISA also accepted. Chocolate chip cookies -encouraged. -
    -
    - -

    1.5 Acknowledgments and citations -

    -

    LAMMPS development has been funded by the US Department of -Energy (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life -programs and its OASCR and OBER offices. -

    -

    Specifically, work on the latest version was funded in part by the US -Department of Energy's Genomics:GTL program -(www.doegenomestolife.org) under the project, "Carbon -Sequestration in Synechococcus Sp.: From Molecular Machines to -Hierarchical Modeling". -

    - - - - - - - - - - -

    The following paper describe the basic parallel algorithms used in -LAMMPS. If you use LAMMPS results in your published work, please cite -this paper and include a pointer to the LAMMPS WWW Site -(http://lammps.sandia.gov): -

    -

    S. J. Plimpton, Fast Parallel Algorithms for Short-Range Molecular -Dynamics, J Comp Phys, 117, 1-19 (1995). -

    -

    Other papers describing specific algorithms used in LAMMPS are listed -under the Citing LAMMPS link of -the LAMMPS WWW page. -

    -

    The Publications link on the -LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is -not listed there for some reason, feel free to send us the info. If -the simulations in your paper produced cool pictures or animations, -we'll be pleased to add them to the -Pictures or -Movies pages of the LAMMPS WWW -site. -

    -

    The core group of LAMMPS developers is at Sandia National Labs: -

    -
    • Steve Plimpton, sjplimp at sandia.gov -
    • Aidan Thompson, athomps at sandia.gov -
    • Paul Crozier, pscrozi at sandia.gov -
    -

    The following folks are responsible for significant contributions to -the code, or other aspects of the LAMMPS development effort. Many of -the packages they have written are somewhat unique to LAMMPS and the -code would not be as general-purpose as it is without their expertise -and efforts. -

    -
    • Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages -
    • Roy Pollock (LLNL), Ewald and PPPM solvers -
    • Mike Brown (ORNL), brownw at ornl.gov, GPU package -
    • Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential -
    • Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics -
    • Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion -
    • Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling -
    • Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD -
    • Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package -
    • Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field -
    • Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling -
    • Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF -
    • Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package -
    -

    As discussed in Section_history, LAMMPS -originated as a cooperative project between DOE labs and industrial -partners. Folks involved in the design and testing of the original -version of LAMMPS were the following: -

    -
    • John Carpenter (Mayo Clinic, formerly at Cray Research) -
    • Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) -
    • Steve Lustig (Dupont) -
    • Jim Belak (LLNL) -
    - diff --git a/doc/doc2/Section_modify.html b/doc/doc2/Section_modify.html deleted file mode 100644 index 737674404a..0000000000 --- a/doc/doc2/Section_modify.html +++ /dev/null @@ -1,798 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands - Next -Section -
    - - - - - - -
    - -

    10. Modifying & extending LAMMPS -

    -

    This section describes how to customize LAMMPS by modifying -and extending its source code. -

    -10.1 Atom styles
    -10.2 Bond, angle, dihedral, improper potentials
    -10.3 Compute styles
    -10.4 Dump styles
    -10.5 Dump custom output options
    -10.6 Fix styles which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
    -10.7 Input script commands
    -10.8 Kspace computations
    -10.9 Minimization styles
    -10.10 Pairwise potentials
    -10.11 Region styles
    -10.12 Body styles
    -10.13 Thermodynamic output options
    -10.14 Variable options
    -10.15 Submitting new features for inclusion in LAMMPS
    - -

    LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% of its source code -is files added in this fashion. -

    -

    In this section, changes and additions users can make are listed along -with minimal instructions. If you add a new feature to LAMMPS and -think it will be of interest to general users, we encourage you to -submit it to the developers for inclusion in the released version of -LAMMPS. Information about how to do this is provided -below. -

    -

    The best way to add a new feature is to find a similar feature in -LAMMPS and look at the corresponding source and header files to figure -out what it does. You will need some knowledge of C++ to be able to -understand the hi-level structure of LAMMPS and its class -organization, but functions (class methods) that do actual -computations are written in vanilla C-style code and operate on simple -C-style data structures (vectors and arrays). -

    -

    Most of the new features described in this section require you to -write a new C++ derived class (except for exceptions described below, -where you can make small edits to existing files). Creating a new -class requires 2 files, a source code file (*.cpp) and a header file -(*.h). The derived class must provide certain methods to work as a -new option. Depending on how different your new feature is compared -to existing features, you can either derive from the base class -itself, or from a derived class that already exists. Enabling LAMMPS -to invoke the new class is as simple as putting the two source -files in the src dir and re-building LAMMPS. -

    -

    The advantage of C++ and its object-orientation is that all the code -and variables needed to define the new feature are in the 2 files you -write, and thus shouldn't make the rest of LAMMPS more complex or -cause side-effect bugs. -

    -

    Here is a concrete example. Suppose you write 2 files pair_foo.cpp -and pair_foo.h that define a new class PairFoo that computes pairwise -potentials described in the classic 1997 paper by Foo, et al. -If you wish to invoke those potentials in a LAMMPS input script with a -command like -

    -
    pair_style foo 0.1 3.5 
-
    -

    then your pair_foo.h file should be structured as follows: -

    -
    #ifdef PAIR_CLASS
-PairStyle(foo,PairFoo)
-#else
-...
-(class definition for PairFoo)
-...
-#endif 
-
    -

    where "foo" is the style keyword in the pair_style command, and -PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h -files. -

    -

    When you re-build LAMMPS, your new pairwise potential becomes part of -the executable and can be invoked with a pair_style command like the -example above. Arguments like 0.1 and 3.5 can be defined and -processed by your new class. -

    -

    As illustrated by this pairwise example, many kinds of options are -referred to in the LAMMPS documentation as the "style" of a particular -command. -

    -

    The instructions below give the header file for the base class that -these styles are derived from. Public variables in that file are ones -used and set by the derived classes which are also used by the base -class. Sometimes they are also used by the rest of LAMMPS. Virtual -functions in the base class header file which are set = 0 are ones you -must define in your new derived class to give it the functionality -LAMMPS expects. Virtual functions that are not set to 0 are functions -you can optionally define. -

    -

    Additionally, new output options can be added directly to the -thermo.cpp, dump_custom.cpp, and variable.cpp files as explained -below. -

    -

    Here are additional guidelines for modifying LAMMPS and adding new -functionality: -

    -
    • Think about whether what you want to do would be better as a pre- or -post-processing step. Many computations are more easily and more -quickly done that way. - -
    • Don't do anything within the timestepping of a run that isn't -parallel. E.g. don't accumulate a bunch of data on a single processor -and analyze it. You run the risk of seriously degrading the parallel -efficiency. - -
    • If your new feature reads arguments or writes output, make sure you -follow the unit conventions discussed by the units -command. - -
    • If you add something you think is truly useful and doesn't impact -LAMMPS performance when it isn't used, send an email to the -developers. We might be -interested in adding it to the LAMMPS distribution. See further -details on this at the bottom of this page. -
    -
    - -
    - -

    10.1 Atom styles -

    -

    Classes that define an atom style are derived from -the AtomVec class and managed by the Atom class. The atom style -determines what attributes are associated with an atom. A new atom -style can be created if one of the existing atom styles does not -define all the attributes you need to store and communicate with -atoms. -

    -

    Atom_vec_atomic.cpp is a simple example of an atom style. -

    -

    Here is a brief description of methods you define in your new derived -class. See atom_vec.h for details. -

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    init one time setup (optional)
    grow re-allocate atom arrays to longer lengths (required)
    grow_reset make array pointers in Atom and AtomVec classes consistent (required)
    copy copy info for one atom to another atom's array locations (required)
    pack_comm store an atom's info in a buffer communicated every timestep (required)
    pack_comm_vel add velocity info to communication buffer (required)
    pack_comm_hybrid store extra info unique to this atom style (optional)
    unpack_comm retrieve an atom's info from the buffer (required)
    unpack_comm_vel also retrieve velocity info (required)
    unpack_comm_hybrid retreive extra info unique to this atom style (optional)
    pack_reverse store an atom's info in a buffer communicating partial forces (required)
    pack_reverse_hybrid store extra info unique to this atom style (optional)
    unpack_reverse retrieve an atom's info from the buffer (required)
    unpack_reverse_hybrid retreive extra info unique to this atom style (optional)
    pack_border store an atom's info in a buffer communicated on neighbor re-builds (required)
    pack_border_vel add velocity info to buffer (required)
    pack_border_hybrid store extra info unique to this atom style (optional)
    unpack_border retrieve an atom's info from the buffer (required)
    unpack_border_vel also retrieve velocity info (required)
    unpack_border_hybrid retreive extra info unique to this atom style (optional)
    pack_exchange store all an atom's info to migrate to another processor (required)
    unpack_exchange retrieve an atom's info from the buffer (required)
    size_restart number of restart quantities associated with proc's atoms (required)
    pack_restart pack atom quantities into a buffer (required)
    unpack_restart unpack atom quantities from a buffer (required)
    create_atom create an individual atom of this style (required)
    data_atom parse an atom line from the data file (required)
    data_atom_hybrid parse additional atom info unique to this atom style (optional)
    data_vel parse one line of velocity information from data file (optional)
    data_vel_hybrid parse additional velocity data unique to this atom style (optional)
    memory_usage tally memory allocated by atom arrays (required) -
    - -

    The constructor of the derived class sets values for several variables -that you must set when defining a new atom style, which are documented -in atom_vec.h. New atom arrays are defined in atom.cpp. Search for -the word "customize" and you will find locations you will need to -modify. -

    -

    IMPORTANT NOTE: It is possible to add some attributes, such as a -molecule ID, to atom styles that do not have them via the fix -property/atom command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the fix -property/atom doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. -

    -

    New pair styles, fixes, or -computes can be added to LAMMPS, as discussed below. -The code for these classes can use the per-atom properties defined by -fix property/atom. The Atom class has a find_custom() method that is -useful in this context: -

    -
    int index = atom->find_custom(char *name, int &flag); 
-
    -

    The "name" of a custom attribute, as specified in the fix -property/atom command, is checked to verify -that it exists and its index is returned. The method also sets flag = -0/1 depending on whether it is an integer or floating-point attribute. -The vector of values associated with the attribute can then be -accessed using the returned index as -

    -
    int *ivector = atom->ivector[index];
-double *dvector = atom->dvector[index]; 
-
    -

    Ivector or dvector are vectors of length Nlocal = # of owned atoms, -which store the attributes of individual atoms. -

    -
    - -

    10.2 Bond, angle, dihedral, improper potentials -

    -

    Classes that compute molecular interactions are derived from the Bond, -Angle, Dihedral, and Improper classes. New styles can be created to -add new potentials to LAMMPS. -

    -

    Bond_harmonic.cpp is the simplest example of a bond style. Ditto for -the harmonic forms of the angle, dihedral, and improper style -commands. -

    -

    Here is a brief description of common methods you define in your -new derived class. See bond.h, angle.h, dihedral.h, and improper.h -for details and specific additional methods. -

    -
    - - - - - - - - - -
    init check if all coefficients are set, calls init_style (optional)
    init_style check if style specific conditions are met (optional)
    compute compute the molecular interactions (required)
    settings apply global settings for all types (optional)
    coeff set coefficients for one type (required)
    equilibrium_distance length of bond, used by SHAKE (required, bond only)
    equilibrium_angle opening of angle, used by SHAKE (required, angle only)
    write & read_restart writes/reads coeffs to restart files (required)
    single force and energy of a single bond or angle (required, bond or angle only)
    memory_usage tally memory allocated by the style (optional) -
    - -
    - -

    10.3 Compute styles -

    -

    Classes that compute scalar and vector quantities like temperature -and the pressure tensor, as well as classes that compute per-atom -quantities like kinetic energy and the centro-symmetry parameter -are derived from the Compute class. New styles can be created -to add new calculations to LAMMPS. -

    -

    Compute_temp.cpp is a simple example of computing a scalar -temperature. Compute_ke_atom.cpp is a simple example of computing -per-atom kinetic energy. -

    -

    Here is a brief description of methods you define in your new derived -class. See compute.h for details. -

    -
    - - - - - - - - - - - - - - - -
    init perform one time setup (required)
    init_list neighbor list setup, if needed (optional)
    compute_scalar compute a scalar quantity (optional)
    compute_vector compute a vector of quantities (optional)
    compute_peratom compute one or more quantities per atom (optional)
    compute_local compute one or more quantities per processor (optional)
    pack_comm pack a buffer with items to communicate (optional)
    unpack_comm unpack the buffer (optional)
    pack_reverse pack a buffer with items to reverse communicate (optional)
    unpack_reverse unpack the buffer (optional)
    remove_bias remove velocity bias from one atom (optional)
    remove_bias_all remove velocity bias from all atoms in group (optional)
    restore_bias restore velocity bias for one atom after remove_bias (optional)
    restore_bias_all same as before, but for all atoms in group (optional)
    pair_tally_callback callback function for tally-style computes (optional).
    memory_usage tally memory usage (optional) -
    - -

    Tally-style computes are a special case, as their computation is done -in two stages: the callback function is registered with the pair style -and then called from the Pair::ev_tally() function, which is called for -each pair after force and energy has been computed for this pair. Then -the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The USER-TALLY package -provides examples_compute_tally.html for utilizing this mechanism. -

    -
    - -

    10.4 Dump styles -

    -

    10.5 Dump custom output options -

    -

    Classes that dump per-atom info to files are derived from the Dump -class. To dump new quantities or in a new format, a new derived dump -class can be added, but it is typically simpler to modify the -DumpCustom class contained in the dump_custom.cpp file. -

    -

    Dump_atom.cpp is a simple example of a derived dump class. -

    -

    Here is a brief description of methods you define in your new derived -class. See dump.h for details. -

    -
    - - - -
    write_header write the header section of a snapshot of atoms
    count count the number of lines a processor will output
    pack pack a proc's output data into a buffer
    write_data write a proc's data to a file -
    - -

    See the dump command and its custom style for a list of -keywords for atom information that can already be dumped by -DumpCustom. It includes options to dump per-atom info from Compute -classes, so adding a new derived Compute class is one way to calculate -new quantities to dump. -

    -

    Alternatively, you can add new keywords to the dump custom command. -Search for the word "customize" in dump_custom.cpp to see the -half-dozen or so locations where code will need to be added. -

    -
    - -

    10.6 Fix styles -

    -

    In LAMMPS, a "fix" is any operation that is computed during -timestepping that alters some property of the system. Essentially -everything that happens during a simulation besides force computation, -neighbor list construction, and output, is a "fix". This includes -time integration (update of coordinates and velocities), force -constraints or boundary conditions (SHAKE or walls), and diagnostics -(compute a diffusion coefficient). New styles can be created to add -new options to LAMMPS. -

    -

    Fix_setforce.cpp is a simple example of setting forces on atoms to -prescribed values. There are dozens of fix options already in LAMMPS; -choose one as a template that is similar to what you want to -implement. -

    -

    Here is a brief description of methods you can define in your new -derived class. See fix.h for details. -

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    setmask determines when the fix is called during the timestep (required)
    init initialization before a run (optional)
    setup_pre_exchange called before atom exchange in setup (optional)
    setup_pre_force called before force computation in setup (optional)
    setup called immediately before the 1st timestep and after forces are computed (optional)
    min_setup_pre_force like setup_pre_force, but for minimizations instead of MD runs (optional)
    min_setup like setup, but for minimizations instead of MD runs (optional)
    initial_integrate called at very beginning of each timestep (optional)
    pre_exchange called before atom exchange on re-neighboring steps (optional)
    pre_neighbor called before neighbor list build (optional)
    pre_force called before pair & molecular forces are computed (optional)
    post_force called after pair & molecular forces are computed and communicated (optional)
    final_integrate called at end of each timestep (optional)
    end_of_step called at very end of timestep (optional)
    write_restart dumps fix info to restart file (optional)
    restart uses info from restart file to re-initialize the fix (optional)
    grow_arrays allocate memory for atom-based arrays used by fix (optional)
    copy_arrays copy atom info when an atom migrates to a new processor (optional)
    pack_exchange store atom's data in a buffer (optional)
    unpack_exchange retrieve atom's data from a buffer (optional)
    pack_restart store atom's data for writing to restart file (optional)
    unpack_restart retrieve atom's data from a restart file buffer (optional)
    size_restart size of atom's data (optional)
    maxsize_restart max size of atom's data (optional)
    setup_pre_force_respa same as setup_pre_force, but for rRESPA (optional)
    initial_integrate_respa same as initial_integrate, but for rRESPA (optional)
    post_integrate_respa called after the first half integration step is done in rRESPA (optional)
    pre_force_respa same as pre_force, but for rRESPA (optional)
    post_force_respa same as post_force, but for rRESPA (optional)
    final_integrate_respa same as final_integrate, but for rRESPA (optional)
    min_pre_force called after pair & molecular forces are computed in minimizer (optional)
    min_post_force called after pair & molecular forces are computed and communicated in minmizer (optional)
    min_store store extra data for linesearch based minimization on a LIFO stack (optional)
    min_pushstore push the minimization LIFO stack one element down (optional)
    min_popstore pop the minimization LIFO stack one element up (optional)
    min_clearstore clear minimization LIFO stack (optional)
    min_step reset or move forward on line search minimization (optional)
    min_dof report number of degrees of freedom added by this fix in minimization (optional)
    max_alpha report maximum allowed step size during linesearch minimization (optional)
    pack_comm pack a buffer to communicate a per-atom quantity (optional)
    unpack_comm unpack a buffer to communicate a per-atom quantity (optional)
    pack_reverse_comm pack a buffer to reverse communicate a per-atom quantity (optional)
    unpack_reverse_comm unpack a buffer to reverse communicate a per-atom quantity (optional)
    dof report number of degrees of freedom removed by this fix during MD (optional)
    compute_scalar return a global scalar property that the fix computes (optional)
    compute_vector return a component of a vector property that the fix computes (optional)
    compute_array return a component of an array property that the fix computes (optional)
    deform called when the box size is changed (optional)
    reset_target called when a change of the target temperature is requested during a run (optional)
    reset_dt is called when a change of the time step is requested during a run (optional)
    modify_param called when a fix_modify request is executed (optional)
    memory_usage report memory used by fix (optional)
    thermo compute quantities for thermodynamic output (optional) -
    - -

    Typically, only a small fraction of these methods are defined for a -particular fix. Setmask is mandatory, as it determines when the fix -will be invoked during the timestep. Fixes that perform time -integration (nve, nvt, npt) implement initial_integrate() and -final_integrate() to perform velocity Verlet updates. Fixes that -constrain forces implement post_force(). -

    -

    Fixes that perform diagnostics typically implement end_of_step(). For -an end_of_step fix, one of your fix arguments must be the variable -"nevery" which is used to determine when to call the fix and you must -set this variable in the constructor of your fix. By convention, this -is the first argument the fix defines (after the ID, group-ID, style). -

    -

    If the fix needs to store information for each atom that persists from -timestep to timestep, it can manage that memory and migrate the info -with the atoms as they move from processors to processor by -implementing the grow_arrays, copy_arrays, pack_exchange, and -unpack_exchange methods. Similarly, the pack_restart and -unpack_restart methods can be implemented to store information about -the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the run_style -command), the initial_integrate, post_force_integrate, and -final_integrate_respa methods can be implemented. The thermo method -enables a fix to contribute values to thermodynamic output, as printed -quantities and/or to be summed to the potential energy of the system. -

    -
    - -

    10.7 Input script commands -

    -

    New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. -

    -

    The single method your new class must define is as follows: -

    -
    -
    command operations performed by the new command -
    - -

    Of course, the new class can define other methods and variables as -needed. -

    -
    - -

    10.8 Kspace computations -

    -

    Classes that compute long-range Coulombic interactions via K-space -representations (Ewald, PPPM) are derived from the KSpace class. New -styles can be created to add new K-space options to LAMMPS. -

    -

    Ewald.cpp is an example of computing K-space interactions. -

    -

    Here is a brief description of methods you define in your new derived -class. See kspace.h for details. -

    -
    - - - -
    init initialize the calculation before a run
    setup computation before the 1st timestep of a run
    compute every-timestep computation
    memory_usage tally of memory usage -
    - -
    - -

    10.9 Minimization styles -

    -

    Classes that perform energy minimization derived from the Min class. -New styles can be created to add new minimization algorithms to -LAMMPS. -

    -

    Min_cg.cpp is an example of conjugate gradient minimization. -

    -

    Here is a brief description of methods you define in your new derived -class. See min.h for details. -

    -
    - - -
    init initialize the minimization before a run
    run perform the minimization
    memory_usage tally of memory usage -
    - -
    - -

    10.10 Pairwise potentials -

    -

    Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include manybody potentials -such as EAM or Tersoff where particles interact without a static bond -topology. New styles can be created to add new pair potentials to -LAMMPS. -

    -

    Pair_lj_cut.cpp is a simple example of a Pair class, though it -includes some optional methods to enable its use with rRESPA. -

    -

    Here is a brief description of the class methods in pair.h: -

    -
    - - - - - - - - -
    compute workhorse routine that computes pairwise interactions
    settings reads the input script line with arguments you define
    coeff set coefficients for one i,j type pair
    init_one perform initialization for one i,j type pair
    init_style initialization specific to this pair style
    write & read_restart write/read i,j pair coeffs to restart files
    write & read_restart_settings write/read global settings to restart files
    single force and energy of a single pairwise interaction between 2 atoms
    compute_inner/middle/outer versions of compute used by rRESPA -
    - -

    The inner/middle/outer routines are optional. -

    -
    - -

    10.11 Region styles -

    -

    Classes that define geometric regions are derived from the Region -class. Regions are used elsewhere in LAMMPS to group atoms, delete -atoms to create a void, insert atoms in a specified region, etc. New -styles can be created to add new region shapes to LAMMPS. -

    -

    Region_sphere.cpp is an example of a spherical region. -

    -

    Here is a brief description of methods you define in your new derived -class. See region.h for details. -

    -
    -
    match determine whether a point is in the region -
    - -
    - -

    10.11 Body styles -

    -

    Classes that define body particles are derived from the Body class. -Body particles can represent complex entities, such as surface meshes -of discrete points, collections of sub-particles, deformable objects, -etc. -

    -

    See Section_howto 14 of the manual for -an overview of using body particles and the body doc page -for details on the various body styles LAMMPS supports. New styles -can be created to add new kinds of body particles to LAMMPS. -

    -

    Body_nparticle.cpp is an example of a body particle that is treated as -a rigid body containing N sub-particles. -

    -

    Here is a brief description of methods you define in your new derived -class. See body.h for details. -

    -
    - - - - - - - -
    data_body process a line from the Bodies section of a data file
    noutrow number of sub-particles output is generated for
    noutcol number of values per-sub-particle output is generated for
    output output values for the Mth sub-particle
    pack_comm_body body attributes to communicate every timestep
    unpack_comm_body unpacking of those attributes
    pack_border_body body attributes to communicate when reneighboring is done
    unpack_border_body unpacking of those attributes -
    - -
    - -

    10.13 Thermodynamic output options -

    -

    There is one class that computes and prints thermodynamic information -to the screen and log file; see the file thermo.cpp. -

    -

    There are two styles defined in thermo.cpp: "one" and "multi". There -is also a flexible "custom" style which allows the user to explicitly -list keywords for quantities to print when thermodynamic info is -output. See the thermo_style command for a list -of defined quantities. -

    -

    The thermo styles (one, multi, etc) are simply lists of keywords. -Adding a new style thus only requires defining a new list of keywords. -Search for the word "customize" with references to "thermo style" in -thermo.cpp to see the two locations where code will need to be added. -

    -

    New keywords can also be added to thermo.cpp to compute new quantities -for output. Search for the word "customize" with references to -"keyword" in thermo.cpp to see the several locations where code will -need to be added. -

    -

    Note that the thermo_style custom command already allows -for thermo output of quantities calculated by fixes, -computes, and variables. Thus, it may -be simpler to compute what you wish via one of those constructs, than -by adding a new keyword to the thermo command. -

    -
    - -

    10.14 Variable options -

    -

    There is one class that computes and stores variable -information in LAMMPS; see the file variable.cpp. The value -associated with a variable can be periodically printed to the screen -via the print, fix print, or -thermo_style custom commands. Variables of style -"equal" can compute complex equations that involve the following types -of arguments: -

    -
    thermo keywords = ke, vol, atoms, ...
-other variables = v_a, v_myvar, ...
-math functions = div(x,y), mult(x,y), add(x,y), ...
-group functions = mass(group), xcm(group,x), ...
-atom values = x[123], y[3], vx[34], ...
-compute values = c_mytemp[0], c_thermo_press[3], ... 
-
    -

    Adding keywords for the thermo_style custom command -(which can then be accessed by variables) was discussed -here on this page. -

    -

    Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaulate() method. Search for -the word "customize" to find the appropriate location. -

    -

    Adding a new group function can be done by editing one section of the -Variable::evaulate() method. Search for the word "customize" to find -the appropriate location. You may need to add a new method to the -Group class as well (see the group.cpp file). -

    -

    Accessing a new atom-based vector can be done by editing one section -of the Variable::evaulate() method. Search for the word "customize" -to find the appropriate location. -

    -

    Adding new compute styles (whose calculated values can -then be accessed by variables) was discussed -here on this page. -

    -
    - -
    - -

    10.15 Submitting new features for inclusion in LAMMPS -

    -

    We encourage users to submit new features to the -developers that they add to -LAMMPS, especially if you think they will be of interest to other -users. If they are broadly useful we may add them as core files to -LAMMPS or as part of a standard package. -Else we will add them as a user-contributed file or package. Examples -of user packages are in src sub-directories that start with USER. The -USER-MISC package is simply a collection of (mostly) unrelated single -files, which is the simplest way to have your contribution quickly -added to the LAMMPS distribution. You can see a list of the both -standard and user packages by typing "make package" in the LAMMPS src -directory. -

    -

    Note that by providing us the files to release, you are agreeing to -make them open-source, i.e. we can release them under the terms of the -GPL, used as a license for the rest of LAMMPS. See Section -1.4 for details. -

    -

    With user packages and files, all we are really providing (aside from -the fame and fortune that accompanies having your name in the source -code and on the Authors page -of the LAMMPS WWW site), is a means for you to distribute your -work to the LAMMPS user community, and a mechanism for others to -easily try out your new feature. This may help you find bugs or make -contact with new collaborators. Note that you're also implicitly -agreeing to support your code which means answer questions, fix bugs, -and maintain it if LAMMPS changes in some way that breaks it (an -unusual event). -

    -

    NOTE: If you prefer to actively develop and support your add-on -feature yourself, then you may wish to make it available for download -from your own website, as a user package that LAMMPS users can add to -their copy of LAMMPS. See the Offsite LAMMPS packages and -tools page of the LAMMPS web -site for examples of groups that do this. We are happy to advertise -your package and web site from that page. Simply email the -developers with info about -your package and we will post it there. -

    -

    The previous sections of this doc page describe how to add new "style" -files of various kinds to LAMMPS. Packages are simply collections of -one or more new class files which are invoked as a new style within a -LAMMPS input script. If designed correctly, these additions typically -do not require changes to the main core of LAMMPS; they are simply -add-on files. If you think your new feature requires non-trivial -changes in core LAMMPS files, you'll need to communicate with the -developers, since we may or may -not want to make those changes. An example of a trivial change is -making a parent-class method "virtual" when you derive a new child -class from it. -

    -

    Here are the steps you need to follow to submit a single file or user -package for our consideration. Following these steps will save both -you and us time. See existing files in packages in the src dir for -examples. -

    -
    • All source files you provide must compile with the most current -version of LAMMPS. - -
    • If you want your file(s) to be added to main LAMMPS or one of its -standard packages, then it needs to be written in a style compatible -with other LAMMPS source files. This is so the developers can -understand it and hopefully maintain it. This basically means that -the code accesses data structures, performs its operations, and is -formatted similar to other LAMMPS source files, including the use of -the error class for error and warning messages. - -
    • If you want your contribution to be added as a user-contributed -feature, and it's a single file (actually a *.cpp and *.h file) it can -rapidly be added to the USER-MISC directory. Send us the one-line -entry to add to the USER-MISC/README file in that dir, along with the -2 source files. You can do this multiple times if you wish to -contribute several individual features. - -
    • If you want your contribution to be added as a user-contribution and -it is several related featues, it is probably best to make it a user -package directory with a name like USER-FOO. In addition to your new -files, the directory should contain a README text file. The README -should contain your name and contact information and a brief -description of what your new package does. If your files depend on -other LAMMPS style files also being installed (e.g. because your file -is a derived class from the other LAMMPS class), then an Install.sh -file is also needed to check for those dependencies. See other README -and Install.sh files in other USER directories as examples. Send us a -tarball of this USER-FOO directory. - -
    • Your new source files need to have the LAMMPS copyright, GPL notice, -and your name and email address at the top, like other -user-contributed LAMMPS source files. They need to create a class -that is inside the LAMMPS namespace. If the file is for one of the -USER packages, including USER-MISC, then we are not as picky about the -coding style (see above). I.e. the files do not need to be in the -same stylistic format and syntax as other LAMMPS files, though that -would be nice for developers as well as users who try to read your -code. - -
    • You must also create a documentation file for each new command or -style you are adding to LAMMPS. This will be one file for a -single-file feature. For a package, it might be several files. These -are simple text files which we auto-convert to HTML. Thus they must -be in the same format as other *.txt files in the lammps/doc directory -for similar commands and styles; use one or more of them as a starting -point. As appropriate, the text files can include links to equations -(see doc/Eqs/*.tex for examples, we auto-create the associated JPG -files), or figures (see doc/JPG for examples), or even additional PDF -files with further details (see doc/PDF for examples). The doc page -should also include literature citations as appropriate; see the -bottom of doc/fix_nh.txt for examples and the earlier part of the same -file for how to format the cite itself. The "Restrictions" section of -the doc page should indicate that your command is only available if -LAMMPS is built with the appropriate USER-MISC or USER-FOO package. -See other user package doc files for examples of how to do this. The -txt2html tool we use to convert to HTML can be downloaded from this -site, so you can perform -the HTML conversion yourself to proofread your doc page. - -
    • For a new package (or even a single command) you can include one or -more example scripts. These should run in no more than 1 minute, even -on a single processor, and not require large data files as input. See -directories under examples/USER for examples of input scripts other -users provided for their packages. - -
    • If there is a paper of yours describing your feature (either the -algorithm/science behind the feature itself, or its initial usage, or -its implementation in LAMMPS), you can add the citation to the *.cpp -source file. See src/USER-EFF/atom_vec_electron.cpp for an example. -A LaTeX citation is stored in a variable at the top of the file and a -single line of code that references the variable is added to the -constructor of the class. Whenever a user invokes your feature from -their input script, this will cause LAMMPS to output the citation to a -log.cite file and prompt the user to examine the file. Note that you -should only use this for a paper you or your group authored. -E.g. adding a cite in the code for a paper by Nose and Hoover if you -write a fix that implements their integrator is not the intended -usage. That kind of citation should just be in the doc page you -provide. -
    -

    Finally, as a general rule-of-thumb, the more clear and -self-explanatory you make your doc and README files, and the easier -you make it for people to get started, e.g. by providing example -scripts, the more likely it is that users will try out your new -feature. -

    -
    - -
    - - - -

    (Foo) Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). -

    - diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html deleted file mode 100644 index 56f1eb3435..0000000000 --- a/doc/doc2/Section_packages.html +++ /dev/null @@ -1,875 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands - Next -Section -
    - - - - - - -
    - -

    4. Packages -

    -

    This section gives a quick overview of the add-on packages that extend -LAMMPS functionality. -

    -4.1 Standard packages
    -4.2 User packages
    - -

    LAMMPS includes many optional packages, which are groups of files that -enable a specific set of features. For example, force fields for -molecular systems or granular systems are in packages. You can see -the list of all packages by typing "make package" from within the src -directory of the LAMMPS distribution. -

    -

    See Section_start 3 of the manual for -details on how to include/exclude specific packages as part of the -LAMMPS build process, and for more details about the differences -between standard packages and user packages. -

    -

    Unless otherwise noted below, every package is independent of all the -others. I.e. any package can be included or excluded in a LAMMPS -build, independent of all other packages. However, note that some -packages include commands derived from commands in other packages. If -the other package is not installed, the derived command from the new -package will also not be installed when you include the new one. -E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package -will not be installed as part of the USER-OMP package if the KSPACE -package is not also installed, since it contains the pair -lj/cut/coul/long command. If you later install the KSPACE pacakge and -the USER-OMP package is already installed, both the pair -lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed. -

    -

    The two tables below list currently available packages in LAMMPS, with -a one-line descriptions of each. The sections below give a few more -details, including instructions for building LAMMPS with the package, -either via the make command or the Make.py tool described in Section -2.4. -

    -
    - -
    - -

    4.1 Standard packages -

    -

    The current list of standard packages is as follows. -

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Package Description Author(s) Doc page Example Library
    ASPHERE aspherical particles - Section_howto 6.14 ellipse -
    BODY body-style particles - body body -
    CLASS2 class 2 force fields - pair_style lj/class2 - -
    COLLOID colloidal particles - atom_style colloid colloid -
    COMPRESS I/O compression Axel Kohlmeyer (Temple U) dump */gz - -
    CORESHELL adiabatic core/shell model Hendrik Heenen (Technical U of Munich) Section_howto 6.25 coreshell -
    DIPOLE point dipole particles - pair_style dipole/cut dipole -
    FLD Fast Lubrication Dynamics Kumar & Bybee & Higdon (1) pair_style lubricateU - -
    GPU GPU-enabled styles Mike Brown (ORNL) Section accelerate gpu lib/gpu
    GRANULAR granular systems - Section_howto 6.6 pour -
    KIM openKIM potentials Smirichinski & Elliot & Tadmor (3) pair_style kim kim KIM
    KOKKOS Kokkos-enabled styles Trott & Edwards (4) Section_accelerate kokkos lib/kokkos
    KSPACE long-range Coulombic solvers - kspace_style peptide -
    MANYBODY many-body potentials - pair_style tersoff shear -
    MEAM modified EAM potential Greg Wagner (Sandia) pair_style meam meam lib/meam
    MC Monte Carlo options - fix gcmc - -
    MOLECULE molecular system force fields - Section_howto 6.3 peptide -
    OPT optimized pair styles Fischer & Richie & Natoli (2) Section accelerate - -
    PERI Peridynamics models Mike Parks (Sandia) pair_style peri peri -
    POEMS coupled rigid body motion Rudra Mukherjee (JPL) fix poems rigid lib/poems
    PYTHON embed Python code in an input script - python python lib/python
    REAX ReaxFF potential Aidan Thompson (Sandia) pair_style reax reax lib/reax
    REPLICA multi-replica methods - Section_howto 6.5 tad -
    RIGID rigid bodies - fix rigid rigid -
    SHOCK shock loading methods - fix msst - -
    SNAP quantum-fit potential Aidan Thompson (Sandia) pair snap snap -
    SRD stochastic rotation dynamics - fix srd srd -
    VORONOI Voronoi tesselations Daniel Schwen (LANL) compute voronoi/atom - Voro++
    XTC dumps in XTC format - dump - -
    -
    - -

    The "Authors" column lists a name(s) if a specific person is -responible for creating and maintaining the package. -More details on -multiple authors are give below. -

    -

    (1) The FLD package was created by Amit Kumar and Michael Bybee from -Jonathan Higdon's group at UIUC. -

    -

    (2) The OPT package was created by James Fischer (High Performance -Technologies), David Richie, and Vincent Natoli (Stone Ridge -Technolgy). -

    -

    (3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott, -and Ellad Tadmor (U Minn). -

    -

    (4) The KOKKOS package was created primarily by Christian Trott -(Sandia). It uses the Kokkos library which was developed by Carter -Edwards, Christian, and collaborators at Sandia. -

    -

    The "Doc page" column links to either a portion of the -Section_howto of the manual, or an input script -command implemented as part of the package. -

    -

    The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory. -

    -

    The "Library" column lists an external library which must be built -first and which LAMMPS links to when it is built. If it is listed as -lib/package, then the code for the library is under the lib directory -of the LAMMPS distribution. See the lib/package/README file for info -on how to build the library. If it is not listed as lib/package, then -it is a third-party library not included in the LAMMPS distribution. -See the src/package/README or src/package/Makefile.lammps file for -info on where to download the library. Section -start of the manual also gives details -on how to build LAMMPS with both kinds of auxiliary libraries. -

    -

    Except where explained below, all of these packages can be installed, -and LAMMPS re-built, by issuing these commands from the src dir. -

    -
    make yes-package
-make machine
-or
-Make.py -p package -a machine 
-
    -

    To un-install the package and re-build LAMMPS without it: -

    -
    make no-package
-make machine
-or
-Make.py -p ^package -a machine 
-
    -

    "Package" is the name of the package in lower-case letters, -e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or -serial. -

    -
    - -
    - -

    Build instructions for COMPRESS package -

    -
    - -

    Build instructions for GPU package -

    -
    - -

    Build instructions for KIM package -

    -
    - -

    Build instructions for KOKKOS package -

    -
    - -

    Build instructions for KSPACE package -

    -
    - -

    Build instructions for MEAM package -

    -
    - -

    Build instructions for POEMS package -

    -
    - -

    Build instructions for PYTHON package -

    -
    - -

    Build instructions for REAX package -

    -
    - -

    Build instructions for VORONOI package -

    -
    - -

    Build instructions for XTC package -

    -
    - -
    - -

    4.2 User packages -

    -

    The current list of user-contributed packages is as follows: -

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Package Description Author(s) Doc page Example Pic/movie Library
    USER-ATC atom-to-continuum coupling Jones & Templeton & Zimmerman (1) fix atc USER/atc atc lib/atc
    USER-AWPMD wave-packet MD Ilya Valuev (JIHT) pair_style awpmd/cut USER/awpmd - lib/awpmd
    USER-CG-CMM coarse-graining model Axel Kohlmeyer (Temple U) pair_style lj/sdk USER/cg-cmm cg -
    USER-COLVARS collective variables Fiorin & Henin & Kohlmeyer (2) fix colvars USER/colvars colvars lib/colvars
    USER-CUDA NVIDIA GPU styles Christian Trott (U Tech Ilmenau) Section accelerate USER/cuda - lib/cuda
    USER-DIFFRACTION virutal x-ray and electron diffraction Shawn Coleman (ARL)compute xrd USER/diffraction - -
    USER-DRUDE Drude oscillators Dequidt & Devemy & Padua (3) tutorial USER/drude - -
    USER-EFF electron force field Andres Jaramillo-Botero (Caltech) pair_style eff/cut USER/eff eff -
    USER-FEP free energy perturbation Agilio Padua (U Blaise Pascal Clermont-Ferrand) compute fep USER/fep - -
    USER-H5MD dump output via HDF5 Pierre de Buyl (KU Leuven) dump h5md - - lib/h5md
    USER-INTEL Vectorized CPU and Intel(R) coprocessor styles W. Michael Brown (Intel) Section accelerate examples/intel - -
    USER-LB Lattice Boltzmann fluid Colin Denniston (U Western Ontario) fix lb/fluid USER/lb - -
    USER-MGPT fast MGPT multi-ion potentials Tomas Oppelstrup & John Moriarty (LLNL) pair_style mgpt USER/mgpt - -
    USER-MISC single-file contributions USER-MISC/README USER-MISC/README - - -
    USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile - - VMD-MOLFILE
    USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate - - -
    USER-PHONON phonon dynamical matrix Ling-Ti Kong (Shanghai Jiao Tong U) fix phonon USER/phonon - -
    USER-QMMM QM/MM coupling Axel Kohlmeyer (Temple U) fix qmmm USER/qmmm - lib/qmmm
    USER-QTB quantum nuclear effects Yuan Shen (Stanford) fix qtb fix_qbmsst qtb - -
    USER-QUIP QUIP/libatoms interface Albert Bartok-Partay (U Cambridge) pair_style quip USER/quip - lib/quip
    USER-REAXC C version of ReaxFF Metin Aktulga (LBNL) pair_style reaxc reax - -
    USER-SMD smoothed Mach dynamics Georg Ganzenmuller (EMI) userguide.pdf USER/smd - -
    USER-SMTBQ Second Moment Tight Binding - QEq potential Salles & Maras & Politano & Tetot (4) pair_style smtbq USER/smtbq - -
    USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf USER/sph sph -
    USER-TALLY Pairwise tallied computes Axel Kohlmeyer (Temple U) compute <...>/tally USER/tally - -
    -
    - - - - - - - - - - - -

    The "Authors" column lists a name(s) if a specific person is -responible for creating and maintaining the package. -

    -

    (1) The ATC package was created by Reese Jones, Jeremy Templeton, and -Jon Zimmerman (Sandia). -

    -

    (2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using -the colvars module library written by Giacomo Fiorin (Temple U) and -Jerome Henin (LISM, Marseille, France). -

    -

    (3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal -Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua -(U Blaise Pascal). -

    -

    (4) The SMTBQ package was created by Nicolas Salles, Emile Maras, -Olivier Politano, and Robert Tetot (LAAS-CNRS, France). -

    -

    If the Library is not listed as lib/package, then it is a third-party -library not included in the LAMMPS distribution. See the -src/package/Makefile.lammps file for info on where to download the -library from. -

    -

    The "Doc page" column links to either a portion of the -Section_howto of the manual, or an input script -command implemented as part of the package, or to additional -documentation provided within the package. -

    -

    The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory. USER/cuda -refers to the examples/USER/cuda directory. -

    -

    The "Library" column lists an external library which must be built -first and which LAMMPS links to when it is built. If it is listed as -lib/package, then the code for the library is under the lib directory -of the LAMMPS distribution. See the lib/package/README file for info -on how to build the library. If it is not listed as lib/package, then -it is a third-party library not included in the LAMMPS distribution. -See the src/package/Makefile.lammps file for info on where to download -the library. Section start of the -manual also gives details on how to build LAMMPS with both kinds of -auxiliary libraries. -

    -

    Except where explained below, all of these packages can be installed, -and LAMMPS re-built, by issuing these commands from the src dir. -

    -
    make yes-user-package
-make machine
-or
-Make.py -p package -a machine 
-
    -

    To un-install the package and re-build LAMMPS without it: -

    -
    make no-user-package
-make machine
-or
-Make.py -p ^package -a machine 
-
    -

    "Package" is the name of the package (in this case without the user -prefix) in lower-case letters, e.g. drude or phonon, and "machine" is -the build target, e.g. mpi or serial. -

    -
    - -
    - -

    USER-ATC package -

    -

    This package implements a "fix atc" command which can be used in a -LAMMPS input script. This fix can be employed to either do concurrent -coupling of MD with FE-based physics surrogates or on-the-fly -post-processing of atomic information to continuum fields. -

    -

    See the doc page for the fix atc command to get started. At the -bottom of the doc page are many links to additional documentation -contained in the doc/USER/atc directory. -

    -

    There are example scripts for using this package in examples/USER/atc. -

    -

    This package uses an external library in lib/atc which must be -compiled before making LAMMPS. See the lib/atc/README file and the -LAMMPS manual for information on building LAMMPS with external -libraries. -

    -

    The primary people who created this package are Reese Jones (rjones at -sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon -Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if -you have questions. -

    -
    - -

    USER-AWPMD package -

    -

    This package contains a LAMMPS implementation of the Antisymmetrized -Wave Packet Molecular Dynamics (AWPMD) method. -

    -

    See the doc page for the pair_style awpmd/cut command to get started. -

    -

    There are example scripts for using this package in examples/USER/awpmd. -

    -

    This package uses an external library in lib/awpmd which must be -compiled before making LAMMPS. See the lib/awpmd/README file and the -LAMMPS manual for information on building LAMMPS with external -libraries. -

    -

    The person who created this package is Ilya Valuev at the JIHT in -Russia (valuev at physik.hu-berlin.de). Contact him directly if you -have questions. -

    -
    - -

    USER-CG-CMM package -

    -

    This package implements 3 commands which can be used in a LAMMPS input -script: -

    -
    • pair_style lj/sdk -
    • pair_style lj/sdk/coul/long -
    • angle_style sdk -
    -

    These styles allow coarse grained MD simulations with the -parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) -(SDK), with extensions to simulate ionic liquids, electrolytes, lipids -and charged amino acids. -

    -

    See the doc pages for these commands for details. -

    -

    There are example scripts for using this package in -examples/USER/cg-cmm. -

    -

    This is the second generation implementation reducing the the clutter -of the previous version. For many systems with electrostatics, it will -be faster to use pair_style hybrid/overlay with lj/sdk and coul/long -instead of the combined lj/sdk/coul/long style. since the number of -charged atom types is usually small. For any other coulomb -interactions this is now required. To exploit this property, the use -of the kspace_style pppm/cg is recommended over regular pppm. For all -new styles, input file backward compatibility is provided. The old -implementation is still available through appending the /old -suffix. These will be discontinued and removed after the new -implementation has been fully validated. -

    -

    The current version of this package should be considered beta -quality. The CG potentials work correctly for "normal" situations, but -have not been testing with all kinds of potential parameters and -simulation systems. -

    -

    The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. -

    -
    - -

    USER-COLVARS package -

    -

    This package implements the "fix colvars" command which can be -used in a LAMMPS input script. -

    -

    This fix allows to use "collective variables" to implement -Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella -Sampling and Restraints. This code consists of two parts: -

    -
    • A portable collective variable module library written and maintained -
    • by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and -
    • Jerome Henin (LISM, CNRS, Marseille, France). This code is located in -
    • the directory lib/colvars and needs to be compiled first. The colvars -
    • fix and an interface layer, exchanges information between LAMMPS and -
    • the collective variable module. -
    -

    See the doc page of fix colvars for more details. -

    -

    There are example scripts for using this package in -examples/USER/colvars -

    -

    This is a very new interface that does not yet support all -features in the module and will see future optimizations -and improvements. The colvars module library is also available -in NAMD has been thoroughly used and tested there. Bugs and -problems are likely due to the interface layers code. -Thus the current version of this package should be considered -beta quality. -

    -

    The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. -

    -
    - -

    USER-CUDA package -

    -

    This package provides acceleration of various LAMMPS pair styles, fix -styles, compute styles, and long-range Coulombics via PPPM for NVIDIA -GPUs. -

    -

    See this section of the manual to get started: -

    -

    Section_accelerate -

    -

    There are example scripts for using this package in -examples/USER/cuda. -

    -

    This package uses an external library in lib/cuda which must be -compiled before making LAMMPS. See the lib/cuda/README file and the -LAMMPS manual for information on building LAMMPS with external -libraries. -

    -

    The person who created this package is Christian Trott at the -University of Technology Ilmenau, Germany (christian.trott at -tu-ilmenau.de). Contact him directly if you have questions. -

    -
    - -

    USER-DIFFRACTION package -

    -

    This package contains the commands neeed to calculate x-ray and -electron diffraction intensities based on kinematic diffraction -theory. -

    -

    See these doc pages and their related commands to get started: -

    - -

    The person who created this package is Shawn P. Coleman -(shawn.p.coleman8.ctr at mail.mil) while at the University of -Arkansas. Contact him directly if you have questions. -

    -
    - -

    USER-DRUDE package -

    -

    This package implements methods for simulating polarizable systems -in LAMMPS using thermalized Drude oscillators. -

    -

    See these doc pages and their related commands to get started: -

    - -

    There are auxiliary tools for using this package in tools/drude. -

    -

    The person who created this package is Alain Dequidt at Universite -Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr) -Contact him directly if you have questions. Co-authors: Julien Devemy, -Agilio Padua. -

    -
    - -

    USER-EFF package -

    -

    This package contains a LAMMPS implementation of the electron Force -Field (eFF) currently under development at Caltech, as described in -A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, -2010. The eFF potential was first introduced by Su and Goddard, in -2007. -

    -

    eFF can be viewed as an approximation to QM wave packet dynamics and -Fermionic molecular dynamics, combining the ability of electronic -structure methods to describe atomic structure, bonding, and chemistry -in materials, and of plasma methods to describe nonequilibrium -dynamics of large systems with a large number of highly excited -electrons. We classify it as a mixed QM-classical approach rather than -a conventional force field method, which introduces QM-based terms (a -spin-dependent repulsion term to account for the Pauli exclusion -principle and the electron wavefunction kinetic energy associated with -the Heisenberg principle) that reduce, along with classical -electrostatic terms between nuclei and electrons, to the sum of a set -of effective pairwise potentials. This makes eFF uniquely suited to -simulate materials over a wide range of temperatures and pressures -where electronically excited and ionized states of matter can occur -and coexist. -

    -

    The necessary customizations to the LAMMPS core are in place to -enable the correct handling of explicit electron properties during -minimization and dynamics. -

    -

    See the doc page for the pair_style eff/cut command to get started. -

    -

    There are example scripts for using this package in -examples/USER/eff. -

    -

    There are auxiliary tools for using this package in tools/eff. -

    -

    The person who created this package is Andres Jaramillo-Botero at -CalTech (ajaramil at wag.caltech.edu). Contact him directly if you -have questions. -

    -
    - -

    USER-FEP package -

    -

    This package provides methods for performing free energy perturbation -simulations with soft-core pair potentials in LAMMPS. -

    -

    See these doc pages and their related commands to get started: -

    - -

    The person who created this package is Agilio Padua at Universite -Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr) -Contact him directly if you have questions. -

    -
    - -

    USER-H5MD package -

    -

    This package contains a dump h5md command for -performing a dump of atom properties in HDF5 format. HDF5 -files are binary, portable and self-describing and can be -examined and used by a variety of auxiliary tools. The output HDF5 -files are structured in a format called H5MD, which was designed to -store molecular data, and can be used and produced by various MD and -MD-related codes. The dump h5md command gives a -citation to a paper describing the format. -

    - - -

    The person who created this package and the underlying H5MD format is -Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him -directly if you have questions. -

    -
    - -

    USER-INTEL package -

    -

    This package provides options for performing neighbor list and -non-bonded force calculations in single, mixed, or double precision -and also a capability for accelerating calculations with an -Intel(R) Xeon Phi(TM) coprocessor. -

    -

    See this section of the manual to get started: -

    -

    Section_accelerate -

    -

    The person who created this package is W. Michael Brown at Intel -(michael.w.brown at intel.com). Contact him directly if you have questions. -

    -
    - -

    USER-LB package -

    -

    This package contains a LAMMPS implementation of a background -Lattice-Boltzmann fluid, which can be used to model MD particles -influenced by hydrodynamic forces. -

    -

    See this doc page and its related commands to get started: -

    -

    fix lb/fluid -

    -

    The people who created this package are Frances Mackay (fmackay at -uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of -Western Ontario. Contact them directly if you have questions. -

    -
    - -

    USER-MGPT package -

    -

    This package contains a fast implementation for LAMMPS of -quantum-based MGPT multi-ion potentials. The MGPT or model GPT method -derives from first-principles DFT-based generalized pseudopotential -theory (GPT) through a series of systematic approximations valid for -mid-period transition metals with nearly half-filled d bands. The -MGPT method was originally developed by John Moriarty at Lawrence -Livermore National Lab (LLNL). -

    -

    In the general matrix representation of MGPT, which can also be -applied to f-band actinide metals, the multi-ion potentials are -evaluated on the fly during a simulation through d- or f-state matrix -multiplication, and the forces that move the ions are determined -analytically. The mgpt pair style in this package calculates forces -and energies using an optimized matrix-MGPT algorithm due to Tomas -Oppelstrup at LLNL. -

    -

    See this doc page to get started: -

    -

    pair_style mgpt -

    -

    The persons who created the USER-MGPT package are Tomas Oppelstrup -(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) -Contact them directly if you have any questions. -

    -
    - -

    USER-MISC package -

    -

    The files in this package are a potpourri of (mostly) unrelated -features contributed to LAMMPS by users. Each feature is a single -pair of files (*.cpp and *.h). -

    -

    More information about each feature can be found by reading its doc -page in the LAMMPS doc directory. The doc page which lists all LAMMPS -input script commands is as follows: -

    -

    Section_commands -

    -

    User-contributed features are listed at the bottom of the fix, -compute, pair, etc sections. -

    -

    The list of features and author of each is given in the -src/USER-MISC/README file. -

    -

    You should contact the author directly if you have specific questions -about the feature or its coding. -

    -
    - -

    USER-MOLFILE package -

    -

    This package contains a dump molfile command which uses molfile -plugins that are bundled with the -VMD molecular visualization and -analysis program, to enable LAMMPS to dump its information in formats -compatible with various molecular simulation tools. -

    -

    The package only provides the interface code, not the plugins. These -can be obtained from a VMD installation which has to match the -platform that you are using to compile LAMMPS for. By adding plugins -to VMD, support for new file formats can be added to LAMMPS (or VMD or -other programs that use them) without having to recompile the -application itself. -

    -

    See this doc page to get started: -

    -

    dump molfile -

    -

    The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. -

    -
    - -

    USER-OMP package -

    -

    This package provides OpenMP multi-threading support and -other optimizations of various LAMMPS pair styles, dihedral -styles, and fix styles. -

    -

    See this section of the manual to get started: -

    -

    Section_accelerate -

    -

    The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. -

    -
    - -

    USER-PHONON package -

    -

    This package contains a fix phonon command that calculates dynamical -matrices, which can then be used to compute phonon dispersion -relations, directly from molecular dynamics simulations. -

    -

    See this doc page to get started: -

    -

    fix phonon -

    -

    The person who created this package is Ling-Ti Kong (konglt at -sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly -if you have questions. -

    -
    - -

    USER-QMMM package -

    -

    This package provides a fix qmmm command which allows LAMMPS to be -used in a QM/MM simulation, currently only in combination with pw.x -code from the Quantum ESPRESSO package. -

    - - -

    The current implementation only supports an ONIOM style mechanical -coupling to the Quantum ESPRESSO plane wave DFT package. -Electrostatic coupling is in preparation and the interface has been -written in a manner that coupling to other QM codes should be possible -without changes to LAMMPS itself. -

    -

    See this doc page to get started: -

    -

    fix qmmm -

    -

    as well as the lib/qmmm/README file. -

    -

    The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. -

    -
    - -

    USER-QTB package -

    -

    This package provides a self-consistent quantum treatment of the -vibrational modes in a classical molecular dynamics simulation. By -coupling the MD simulation to a colored thermostat, it introduces zero -point energy into the system, alter the energy power spectrum and the -heat capacity towards their quantum nature. This package could be of -interest if one wants to model systems at temperatures lower than -their classical limits or when temperatures ramp up across the -classical limits in the simulation. -

    -

    See these two doc pages to get started: -

    -

    fix qtb provides quantum nulcear correction through a -colored thermostat and can be used with other time integration schemes -like fix nve or fix nph. -

    -

    fix qbmsst enables quantum nuclear correction of a -multi-scale shock technique simulation by coupling the quantum thermal -bath with the shocked system. -

    -

    The person who created this package is Yuan Shen (sy0302 at -stanford.edu) at Stanford University. Contact him directly if you -have questions. -

    -
    - -

    USER-REAXC package -

    -

    This package contains a implementation for LAMMPS of the ReaxFF force -field. ReaxFF uses distance-dependent bond-order functions to -represent the contributions of chemical bonding to the potential -energy. It was originally developed by Adri van Duin and the Goddard -group at CalTech. -

    -

    The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in -C, should give identical or very similar results to pair_style reax, -which is a ReaxFF implementation on top of a Fortran library, a -version of which library was originally authored by Adri van Duin. -

    -

    The reax/c version should be somewhat faster and more scalable, -particularly with respect to the charge equilibration calculation. It -should also be easier to build and use since there are no complicating -issues with Fortran memory allocation or linking to a Fortran library. -

    -

    For technical details about this implemention of ReaxFF, see -this paper: -

    -

    Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods -and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty, -S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011). -

    -

    See the doc page for the pair_style reax/c command for details -of how to use it in LAMMPS. -

    -

    The person who created this package is Hasan Metin Aktulga (hmaktulga -at lbl.gov), while at Purdue University. Contact him directly, or -Aidan Thompson at Sandia (athomps at sandia.gov), if you have -questions. -

    -
    - -

    USER-SMD package -

    -

    This package implements smoothed Mach dynamics (SMD) in -LAMMPS. Currently, the package has the following features: -

    -

    * Does liquids via traditional Smooth Particle Hydrodynamics (SPH) -

    -

    * Also solves solids mechanics problems via a state of the art - stabilized meshless method with hourglass control. -

    -

    * Can specify hydrostatic interactions independently from material - strength models, i.e. pressure and deviatoric stresses are separated. -

    -

    * Many material models available (Johnson-Cook, plasticity with - hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new - material models. -

    -

    * Rigid boundary conditions (walls) can be loaded as surface geometries - from *.STL files. -

    -

    See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started. -

    -

    There are example scripts for using this package in examples/USER/smd. -

    -

    The person who created this package is Georg Ganzenmuller at the -Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in -Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if -you have questions. -

    -
    - -

    USER-SMTBQ package -

    -

    This package implements the Second Moment Tight Binding - QEq (SMTB-Q) -potential for the description of ionocovalent bonds in oxides. -

    -

    There are example scripts for using this package in -examples/USER/smtbq. -

    -

    See this doc page to get started: -

    -

    pair_style smtbq -

    -

    The persons who created the USER-SMTBQ package are Nicolas Salles, -Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at -these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact -them directly if you have any questions. -

    -
    - -

    USER-SPH package -

    -

    This package implements smoothed particle hydrodynamics (SPH) in -LAMMPS. Currently, the package has the following features: -

    -

    * Tait, ideal gas, Lennard-Jones equation of states, full support for - complete (i.e. internal-energy dependent) equations of state -

    -

    * Plain or Monaghans XSPH integration of the equations of motion -

    -

    * Density continuity or density summation to propagate the density field -

    -

    * Commands to set internal energy and density of particles from the - input script -

    -

    * Output commands to access internal energy and density for dumping and - thermo output -

    -

    See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started. -

    -

    There are example scripts for using this package in examples/USER/sph. -

    -

    The person who created this package is Georg Ganzenmuller at the -Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in -Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if -you have questions. -

    - diff --git a/doc/doc2/Section_perf.html b/doc/doc2/Section_perf.html deleted file mode 100644 index 330d99407a..0000000000 --- a/doc/doc2/Section_perf.html +++ /dev/null @@ -1,84 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
    - - - - - - -
    - -

    8. Performance & scalability -

    -

    LAMMPS performance on several prototypical benchmarks and machines is -discussed on the Benchmarks page of the LAMMPS WWW Site where -CPU timings and parallel efficiencies are listed. Here, the -benchmarks are described briefly and some useful rules of thumb about -their performance are highlighted. -

    -

    These are the 5 benchmark problems: -

    -
    1. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 -neighbors per atom), NVE integration - -
    2. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ -pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per -atom), NVE integration - -
    3. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 -neighbors per atom), NVE integration - -
    4. Chute = granular chute flow, frictional history potential with 1.1 -sigma cutoff (7 neighbors per atom), NVE integration - -
    5. Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force -field with a 10 Angstrom LJ cutoff (440 neighbors per atom), -particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT -integration -
    -

    The input files for running the benchmarks are included in the LAMMPS -distribution, as are sample output files. Each of the 5 problems has -32,000 atoms and runs for 100 timesteps. Each can be run as a serial -benchmarks (on one processor) or in parallel. In parallel, each -benchmark can be run as a fixed-size or scaled-size problem. For -fixed-size benchmarking, the same 32K atom problem is run on various -numbers of processors. For scaled-size benchmarking, the model size -is increased with the number of processors. E.g. on 8 processors, a -256K-atom problem is run; on 1024 processors, a 32-million atom -problem is run, etc. -

    -

    A useful metric from the benchmarks is the CPU cost per atom per -timestep. Since LAMMPS performance scales roughly linearly with -problem size and timesteps, the run time of any problem using the same -model (atom style, force field, cutoff, etc) can then be estimated. -For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler -under Red Hat Linux), the CPU run-time in seconds/atom/timestep for -the 5 problems is -

    -
    - - -
    Problem: LJ Chain EAM Chute Rhodopsin
    CPU/atom/step: 4.55E-6 2.18E-6 9.38E-6 2.18E-6 1.11E-4
    Ratio to LJ: 1.0 0.48 2.06 0.48 24.5 -
    - -

    The ratios mean that if the atomic LJ system has a normalized cost of -1.0, the bead-spring chains and granular systems run 2x faster, while -the EAM metal and solvated protein models run 2x and 25x slower -respectively. The bulk of these cost differences is due to the -expense of computing a particular pairwise force field for a given -number of neighbors per atom. -

    -

    Performance on a parallel machine can also be predicted from the -one-processor timings if the parallel efficiency can be estimated. -The communication bandwidth and latency of a particular parallel -machine affects the efficiency. On most machines LAMMPS will give -fixed-size parallel efficiencies on these benchmarks above 50% so long -as the atoms/processor count is a few 100 or greater - i.e. on 64 to -128 processors. Likewise, scaled-size parallel efficiencies will -typically be 80% or greater up to very large processor counts. The -benchmark data on the LAMMPS WWW Site gives specific examples on -some different machines, including a run of 3/4 of a billion LJ atoms -on 1500 processors that ran at 85% parallel efficiency. -

    - diff --git a/doc/doc2/Section_python.html b/doc/doc2/Section_python.html deleted file mode 100644 index bcc34797cc..0000000000 --- a/doc/doc2/Section_python.html +++ /dev/null @@ -1,794 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
    - - - - - - -
    - -

    11. Python interface to LAMMPS -

    -

    LAMMPS can work together with Python in two ways. First, Python can -wrap LAMMPS through the LAMMPS library -interface, so that a Python script can -create one or more instances of LAMMPS and launch one or more -simulations. In Python lingo, this is "extending" Python with LAMMPS. -

    -

    Second, LAMMPS can use the Python interpreter, so that a LAMMPS input -script can invoke Python code, and pass information back-and-forth -between the input script and Python functions you write. The Python -code can also callback to LAMMPS to query or change its attributes. -In Python lingo, this is "embedding" Python in LAMMPS. -

    -

    This section describes how to do both. -

    - -

    If you are not familiar with it, Python is a -powerful scripting and programming language which can essentially do -anything that faster, lower-level languages like C or C++ can do, but -typically with much fewer lines of code. When used in embedded mode, -Python can perform operations that the simplistic LAMMPS input script -syntax cannot. Python can be also be used as a "glue" language to -drive a program through its library interface, or to hook multiple -pieces of software together, such as a simulation package plus a -visualization package, or to run a coupled multiscale or multiphysics -model. -

    -

    See Section_howto 10 of the manual and -the couple directory of the distribution for more ideas about coupling -LAMMPS to other codes. See Section_howto -19 for a description of the LAMMPS -library interface provided in src/library.cpp and src/library.h, and -how to extend it for your needs. As described below, that interface -is what is exposed to Python either when calling LAMMPS from Python or -when calling Python from a LAMMPS input script and then calling back -to LAMMPS from Python code. The library interface is designed to be -easy to add functions to. Thus the Python interface to LAMMPS is also -easy to extend as well. -

    -

    If you create interesting Python scripts that run LAMMPS or -interesting Python functions that can be called from a LAMMPS input -script, that you think would be useful to other users, please email -them to the developers. We can -include them in the LAMMPS distribution. -

    -
    - -
    - -

    11.1 Overview of running LAMMPS from Python -

    -

    The LAMMPS distribution includes a python directory with all you need -to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS -library interface, with one wrapper function per LAMMPS library -function. This file makes it is possible to do the following either -from a Python script, or interactively from a Python prompt: create -one or more instances of LAMMPS, invoke LAMMPS commands or give it an -input script, run LAMMPS incrementally, extract LAMMPS results, an -modify internal LAMMPS variables. From a Python script you can do -this in serial or parallel. Running Python interactively in parallel -does not generally work, unless you have a version of Python that -extends standard Python to enable multiple instances of Python to read -what you type. -

    -

    To do all of this, you must first build LAMMPS as a shared library, -then insure that your Python can find the python/lammps.py file and -the shared library. These steps are explained in subsequent sections -11.3 and 11.4. Sections 11.5 and 11.6 discuss using MPI from a -parallel Python program and how to test that you are ready to use -LAMMPS from Python. Section 11.7 lists all the functions in the -current LAMMPS library interface and how to call them from Python. -

    -

    Section 11.8 gives some examples of coupling LAMMPS to other tools via -Python. For example, LAMMPS can easily be coupled to a GUI or other -visualization tools that display graphs or animations in real time as -LAMMPS runs. Examples of such scripts are inlcluded in the python -directory. -

    -

    Two advantages of using Python to run LAMMPS are how concise the -language is, and that it can be run interactively, enabling rapid -development and debugging of programs. If you use it to mostly invoke -costly operations within LAMMPS, such as running a simulation for a -reasonable number of timesteps, then the overhead cost of invoking -LAMMPS thru Python will be negligible. -

    -

    The Python wrapper for LAMMPS uses the amazing and magical (to me) -"ctypes" package in Python, which auto-generates the interface code -needed between Python and a set of C interface routines for a library. -Ctypes is part of standard Python for versions 2.5 and later. You can -check which version of Python you have installed, by simply typing -"python" at a shell prompt. -

    -
    - -

    11.2 Overview of using Python from a LAMMPS script -

    -

    IMPORTANT NOTE: It is not currently possible to use the -python command described in this section with Python 3, -only with Python 2. The C API changed from Python 2 to 3 and the -LAMMPS code is not compatible with both. -

    -

    LAMMPS has a python command which can be used in an -input script to define and execute a Python function that you write -the code for. The Python function can also be assigned to a LAMMPS -python-style variable via the variable command. Each -time the variable is evaluated, either in the LAMMPS input script -itself, or by another LAMMPS command that uses the variable, this will -trigger the Python function to be invoked. -

    -

    The Python code for the function can be included directly in the input -script or in an auxiliary file. The function can have arguments which -are mapped to LAMMPS variables (also defined in the input script) and -it can return a value to a LAMMPS variable. This is thus a mechanism -for your input script to pass information to a piece of Python code, -ask Python to execute the code, and return information to your input -script. -

    -

    Note that a Python function can be arbitrarily complex. It can import -other Python modules, instantiate Python classes, call other Python -functions, etc. The Python code that you provide can contain more -code than the single function. It can contain other functions or -Python classes, as well as global variables or other mechanisms for -storing state between calls from LAMMPS to the function. -

    -

    The Python function you provide can consist of "pure" Python code that -only performs operations provided by standard Python. However, the -Python function can also "call back" to LAMMPS through its -Python-wrapped library interface, in the manner described in the -previous section 11.1. This means it can issue LAMMPS input script -commands or query and set internal LAMMPS state. As an example, this -can be useful in an input script to create a more complex loop with -branching logic, than can be created using the simple looping and -brancing logic enabled by the next and if -commands. -

    -

    See the python doc page and the variable -doc page for its python-style variables for more info, including -examples of Python code you can write for both pure Python operations -and callbacks to LAMMPS. -

    -

    To run pure Python code from LAMMPS, you only need to build LAMMPS -with the PYTHON package installed: -

    -

    make yes-python -make machine -

    -

    Note that this will link LAMMPS with the Python library on your -system, which typically requires several auxiliary system libraries to -also be linked. The list of these libraries and the paths to find -them are specified in the lib/python/Makefile.lammps file. You need -to insure that file contains the correct information for your version -of Python and your machine to successfully build LAMMPS. See the -lib/python/README file for more info. -

    -

    If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps overviewed in the preceeding section (11.1) -for running LAMMPS from Python. I.e. you must build LAMMPS as a -shared library and insure that Python can find the python/lammps.py -file and the shared library. -

    -
    - -

    11.3 Building LAMMPS as a shared library -

    -

    Instructions on how to build LAMMPS as a shared library are given in -Section_start 5. A shared library is one -that is dynamically loadable, which is what Python requires to wrap -LAMMPS. On Linux this is a library file that ends in ".so", not ".a". -

    -

    >From the src directory, type -

    -
    make foo mode=shlib 
-
    -

    where foo is the machine target name, such as linux or g++ or serial. -This should create the file liblammps_foo.so in the src directory, as -well as a soft link liblammps.so, which is what the Python wrapper will -load by default. Note that if you are building multiple machine -versions of the shared library, the soft link is always set to the -most recently built version. -

    -

    If this fails, see Section_start 5 for -more details, especially if your LAMMPS build uses auxiliary libraries -like MPI or FFTW which may not be built as shared libraries on your -system. -

    -
    - -

    11.4 Installing the Python wrapper into Python -

    -

    For Python to invoke LAMMPS, there are 2 files it needs to know about: -

    -
    • python/lammps.py -
    • src/liblammps.so -
    -

    Lammps.py is the Python wrapper on the LAMMPS library interface. -Liblammps.so is the shared LAMMPS library that Python loads, as -described above. -

    -

    You can insure Python can find these files in one of two ways: -

    -
    • set two environment variables -
    • run the python/install.py script -
    -

    If you set the paths to these files as environment variables, you only -have to do it once. For the csh or tcsh shells, add something like -this to your ~/.cshrc file, one line for each of the two files: -

    -
    setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
-setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src 
-
    -

    If you use the python/install.py script, you need to invoke it every -time you rebuild LAMMPS (as a shared library) or make changes to the -python/lammps.py file. -

    -

    You can invoke install.py from the python directory as -

    -
    % python install.py [libdir] [pydir] 
-
    -

    The optional libdir is where to copy the LAMMPS shared library to; the -default is /usr/local/lib. The optional pydir is where to copy the -lammps.py file to; the default is the site-packages directory of the -version of Python that is running the install script. -

    -

    Note that libdir must be a location that is in your default -LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a -location that Python looks in by default for imported modules, like -its site-packages dir. If you want to copy these files to -non-standard locations, such as within your own user space, you will -need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables -accordingly, as above. -

    -

    If the install.py script does not allow you to copy files into system -directories, prefix the python command with "sudo". If you do this, -make sure that the Python that root runs is the same as the Python you -run. E.g. you may need to do something like -

    -
    % sudo /usr/local/bin/python install.py [libdir] [pydir] 
-
    -

    You can also invoke install.py from the make command in the src -directory as -

    -
    % make install-python 
-
    -

    In this mode you cannot append optional arguments. Again, you may -need to prefix this with "sudo". In this mode you cannot control -which Python is invoked by root. -

    -

    Note that if you want Python to be able to load different versions of -the LAMMPS shared library (see this section below), you will -need to manually copy files like liblammps_g++.so into the appropriate -system directory. This is not needed if you set the LD_LIBRARY_PATH -environment variable as described above. -

    -
    - -

    11.5 Extending Python with MPI to run in parallel -

    -

    If you wish to run LAMMPS in parallel from Python, you need to extend -your Python with an interface to MPI. This also allows you to -make MPI calls directly from Python in your script, if you desire. -

    -

    There are several Python packages available that purport to wrap MPI -as a library and allow MPI functions to be called from Python. -

    -

    These include -

    - -

    All of these except pyMPI work by wrapping the MPI library and -exposing (some portion of) its interface to your Python script. This -means Python cannot be used interactively in parallel, since they do -not address the issue of interactive input to multiple instances of -Python running on different processors. The one exception is pyMPI, -which alters the Python interpreter to address this issue, and (I -believe) creates a new alternate executable (in place of "python" -itself) as a result. -

    -

    In principle any of these Python/MPI packages should work to invoke -LAMMPS in parallel and to make MPI calls themselves from a Python -script which is itself running in parallel. However, when I -downloaded and looked at a few of them, their documentation was -incomplete and I had trouble with their installation. It's not clear -if some of the packages are still being actively developed and -supported. -

    -

    The one I recommend, since I have successfully used it with LAMMPS, is -Pypar. Pypar requires the ubiquitous Numpy -package be installed in your Python. After -launching python, type -

    -
    import numpy 
-
    -

    to see if it is installed. If not, here is how to install it (version -1.3.0b1 as of April 2009). Unpack the numpy tarball and from its -top-level directory, type -

    -
    python setup.py build
-sudo python setup.py install 
-
    -

    The "sudo" is only needed if required to copy Numpy files into your -Python distribution's site-packages directory. -

    -

    To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it -and from its "source" directory, type -

    -
    python setup.py build
-sudo python setup.py install 
-
    -

    Again, the "sudo" is only needed if required to copy Pypar files into -your Python distribution's site-packages directory. -

    -

    If you have successully installed Pypar, you should be able to run -Python and type -

    -
    import pypar 
-
    -

    without error. You should also be able to run python in parallel -on a simple test script -

    -
    % mpirun -np 4 python test.py 
-
    -

    where test.py contains the lines -

    -
    import pypar
-print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) 
-
    -

    and see one line of output for each processor you run on. -

    -

    IMPORTANT NOTE: To use Pypar and LAMMPS in parallel from Python, you -must insure both are using the same version of MPI. If you only have -one MPI installed on your system, this is not an issue, but it can be -if you have multiple MPIs. Your LAMMPS build is explicit about which -MPI it is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. Pypar uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both Pypar and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that Pypar finds -the right one. -

    -
    - -

    11.6 Testing the Python-LAMMPS interface -

    -

    To test if LAMMPS is callable from Python, launch Python interactively -and type: -

    -
    >>> from lammps import lammps
->>> lmp = lammps() 
-
    -

    If you get no errors, you're ready to use LAMMPS from Python. If the -2nd command fails, the most common error to see is -

    -
    OSError: Could not load LAMMPS dynamic library 
-
    -

    which means Python was unable to load the LAMMPS shared library. This -typically occurs if the system can't find the LAMMPS shared library or -one of the auxiliary shared libraries it depends on, or if something -about the library is incompatible with your Python. The error message -should give you an indication of what went wrong. -

    -

    You can also test the load directly in Python as follows, without -first importing from the lammps.py file: -

    -
    >>> from ctypes import CDLL
->>> CDLL("liblammps.so") 
-
    -

    If an error occurs, carefully go thru the steps in Section_start -5 and above about building a shared -library and about insuring Python can find the necessary two files -it needs. -

    -
    Test LAMMPS and Python in serial: -
    -

    To run a LAMMPS test in serial, type these lines into Python -interactively from the bench directory: -

    -
    >>> from lammps import lammps
->>> lmp = lammps()
->>> lmp.file("in.lj") 
-
    -

    Or put the same lines in the file test.py and run it as -

    -
    % python test.py 
-
    -

    Either way, you should see the results of running the in.lj benchmark -on a single processor appear on the screen, the same as if you had -typed something like: -

    -
    lmp_g++ -in in.lj 
-
    -
    Test LAMMPS and Python in parallel: -
    -

    To run LAMMPS in parallel, assuming you have installed the -Pypar package as discussed -above, create a test.py file containing these lines: -

    -
    import pypar
-from lammps import lammps
-lmp = lammps()
-lmp.file("in.lj")
-print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
-pypar.finalize() 
-
    -

    You can then run it in parallel as: -

    -
    % mpirun -np 4 python test.py 
-
    -

    and you should see the same output as if you had typed -

    -
    % mpirun -np 4 lmp_g++ -in in.lj 
-
    -

    Note that if you leave out the 3 lines from test.py that specify Pypar -commands you will instantiate and run LAMMPS independently on each of -the P processors specified in the mpirun command. In this case you -should get 4 sets of output, each showing that a LAMMPS run was made -on a single processor, instead of one set of output showing that -LAMMPS ran on 4 processors. If the 1-processor outputs occur, it -means that Pypar is not working correctly. -

    -

    Also note that once you import the PyPar module, Pypar initializes MPI -for you, and you can use MPI calls directly in your Python script, as -described in the Pypar documentation. The last line of your Python -script should be pypar.finalize(), to insure MPI is shut down -correctly. -

    -
    Running Python scripts: -
    -

    Note that any Python script (not just for LAMMPS) can be invoked in -one of several ways: -

    -
    % python foo.script
-% python -i foo.script
-% foo.script 
-
    -

    The last command requires that the first line of the script be -something like this: -

    -
    #!/usr/local/bin/python 
-#!/usr/local/bin/python -i 
-
    -

    where the path points to where you have Python installed, and that you -have made the script file executable: -

    -
    % chmod +x foo.script 
-
    -

    Without the "-i" flag, Python will exit when the script finishes. -With the "-i" flag, you will be left in the Python interpreter when -the script finishes, so you can type subsequent commands. As -mentioned above, you can only run Python interactively when running -Python on a single processor, not in parallel. -

    -
    - -
    - -

    11.7 Using LAMMPS from Python -

    -

    As described above, the Python interface to LAMMPS consists of a -Python "lammps" module, the source code for which is in -python/lammps.py, which creates a "lammps" object, with a set of -methods that can be invoked on that object. The sample Python code -below assumes you have first imported the "lammps" module in your -Python script, as follows: -

    -
    from lammps import lammps 
-
    -

    These are the methods defined by the lammps module. If you look at -the files src/library.cpp and src/library.h you will see that they -correspond one-to-one with calls you can make to the LAMMPS library -from a C++ or C or Fortran program. -

    -
    lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-lmp = lammps(ptr=lmpptr) # ditto, but use lmpptr as previously created LAMMPS object
-lmp = lammps("g++")      # create a LAMMPS object using the liblammps_g++.so library
-lmp = lammps("",list)    # ditto, with command-line args, e.g. list = ["-echo","screen"]
-lmp = lammps("g++",list) 
-
    -
    lmp.close()              # destroy a LAMMPS object 
-
    -

    version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 -

    -
    lmp.file(file)           # run an entire input script, file = "in.lj"
-lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" 
-
    -
    xlo = lmp.extract_global(name,type)  # extract a global quantity
-                                     # name = "boxxlo", "nlocal", etc
-				     # type = 0 = int
-				     #        1 = double 
-
    -
    coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
-                                          # name = "x", "type", etc
-				          # type = 0 = vector of ints
-				          #        1 = array of ints
-				          #        2 = vector of doubles
-				          #        3 = array of doubles 
-
    -
    eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
-v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
-                                          # id = ID of compute or fix
-					  # style = 0 = global data
-					  #	    1 = per-atom data
-					  #         2 = local data
-					  # type = 0 = scalar
-					  #	   1 = vector
-					  #        2 = array
-					  # i,j = indices of value in global vector or array 
-
    -
    var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
-	                                     # name = name of variable
-					     # group = group ID (ignored for equal-style variables)
-					     # flag = 0 = equal-style variable
-					     #        1 = atom-style variable 
-
    -
    flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
-natoms = lmp.get_natoms()                 # total # of atoms as int
-data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc
-lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms from data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc 
-
    -
    - -

    IMPORTANT NOTE: Currently, the creation of a LAMMPS object from within -lammps.py does not take an MPI communicator as an argument. There -should be a way to do this, so that the LAMMPS instance runs on a -subset of processors if desired, but I don't know how to do it from -Pypar. So for now, it runs with MPI_COMM_WORLD, which is all the -processors. If someone figures out how to do this with one or more of -the Python wrappers for MPI, like Pypar, please let us know and we -will amend these doc pages. -

    -

    The lines -

    -
    from lammps import lammps
-lmp = lammps() 
-
    -

    create an instance of LAMMPS, wrapped in a Python class by the lammps -Python module, and return an instance of the Python class as lmp. It -is used to make all subequent calls to the LAMMPS library. -

    -

    Additional arguments can be used to tell Python the name of the shared -library to load or to pass arguments to the LAMMPS instance, the same -as if LAMMPS were launched from a command-line prompt. -

    -

    If the ptr argument is set like this: -

    -
    lmp = lammps(ptr=lmpptr) 
-
    -

    then lmpptr must be an argument passed to Python via the LAMMPS -python command, when it is used to define a Python -function that is invoked by the LAMMPS input script. This mode of -using Python with LAMMPS is described above in 11.2. The variable -lmpptr refers to the instance of LAMMPS that called the embedded -Python interpreter. Using it as an argument to lammps() allows the -returned Python class instance "lmp" to make calls to that instance of -LAMMPS. See the python command doc page for examples -using this syntax. -

    -

    Note that you can create multiple LAMMPS objects in your Python -script, and coordinate and run multiple simulations, e.g. -

    -
    from lammps import lammps
-lmp1 = lammps()
-lmp2 = lammps()
-lmp1.file("in.file1")
-lmp2.file("in.file2") 
-
    -

    The file() and command() methods allow an input script or single -commands to be invoked. -

    -

    The extract_global(), extract_atom(), extract_compute(), -extract_fix(), and extract_variable() methods return values or -pointers to data structures internal to LAMMPS. -

    -

    For extract_global() see the src/library.cpp file for the list of -valid names. New names could easily be added. A double or integer is -returned. You need to specify the appropriate data type via the type -argument. -

    -

    For extract_atom(), a pointer to internal LAMMPS atom-based data is -returned, which you can use via normal Python subscripting. See the -extract() method in the src/atom.cpp file for a list of valid names. -Again, new names could easily be added. A pointer to a vector of -doubles or integers, or a pointer to an array of doubles (double **) -or integers (int **) is returned. You need to specify the appropriate -data type via the type argument. -

    -

    For extract_compute() and extract_fix(), the global, per-atom, or -local data calulated by the compute or fix can be accessed. What is -returned depends on whether the compute or fix calculates a scalar or -vector or array. For a scalar, a single double value is returned. If -the compute or fix calculates a vector or array, a pointer to the -internal LAMMPS data is returned, which you can use via normal Python -subscripting. The one exception is that for a fix that calculates a -global vector or array, a single double value from the vector or array -is returned, indexed by I (vector) or I and J (array). I,J are -zero-based indices. The I,J arguments can be left out if not needed. -See Section_howto 15 of the manual for a -discussion of global, per-atom, and local data, and of scalar, vector, -and array data types. See the doc pages for individual -computes and fixes for a description of what -they calculate and store. -

    -

    For extract_variable(), an equal-style or atom-style -variable is evaluated and its result returned. -

    -

    For equal-style variables a single double value is returned and the -group argument is ignored. For atom-style variables, a vector of -doubles is returned, one value per atom, which you can use via normal -Python subscripting. The values will be zero for atoms not in the -specified group. -

    -

    The get_natoms() method returns the total number of atoms in the -simulation, as an int. -

    -

    The gather_atoms() method returns a ctypes vector of ints or doubles -as specified by type, of length count*natoms, for the property of all -the atoms in the simulation specified by name, ordered by count and -then by atom ID. The vector can be used via normal Python -subscripting. If atom IDs are not consecutively ordered within -LAMMPS, a None is returned as indication of an error. -

    -

    Note that the data structure gather_atoms("x") returns is different -from the data structure returned by extract_atom("x") in four ways. -(1) Gather_atoms() returns a vector which you index as x[i]; -extract_atom() returns an array which you index as x[i][j]. (2) -Gather_atoms() orders the atoms by atom ID while extract_atom() does -not. (3) Gathert_atoms() returns a list of all atoms in the -simulation; extract_atoms() returns just the atoms local to each -processor. (4) Finally, the gather_atoms() data structure is a copy -of the atom coords stored internally in LAMMPS, whereas extract_atom() -returns an array that effectively points directly to the internal -data. This means you can change values inside LAMMPS from Python by -assigning a new values to the extract_atom() array. To do this with -the gather_atoms() vector, you need to change values in the vector, -then invoke the scatter_atoms() method. -

    -

    The scatter_atoms() method takes a vector of ints or doubles as -specified by type, of length count*natoms, for the property of all the -atoms in the simulation specified by name, ordered by bount and then -by atom ID. It uses the vector of data to overwrite the corresponding -properties for each atom inside LAMMPS. This requires LAMMPS to have -its "map" option enabled; see the atom_modify -command for details. If it is not, or if atom IDs are not -consecutively ordered, no coordinates are reset. -

    -

    The array of coordinates passed to scatter_atoms() must be a ctypes -vector of ints or doubles, allocated and initialized something like -this: -

    -
    from ctypes import *
-natoms = lmp.get_natoms()
-n3 = 3*natoms
-x = (n3*c_double)()
-x[0] = x coord of atom with ID 1
-x[1] = y coord of atom with ID 1
-x[2] = z coord of atom with ID 1
-x[3] = x coord of atom with ID 2
-...
-x[n3-1] = z coord of atom with ID natoms
-lmp.scatter_coords("x",1,3,x) 
-
    -

    Alternatively, you can just change values in the vector returned by -gather_atoms("x",1,3), since it is a ctypes vector of doubles. -

    -
    - -

    As noted above, these Python class methods correspond one-to-one with -the functions in the LAMMPS library interface in src/library.cpp and -library.h. This means you can extend the Python wrapper via the -following steps: -

    -
    • Add a new interface function to src/library.cpp and -src/library.h. - -
    • Rebuild LAMMPS as a shared library. - -
    • Add a wrapper method to python/lammps.py for this interface -function. - -
    • You should now be able to invoke the new interface function from a -Python script. Isn't ctypes amazing? -
    -
    - -
    - -

    11.8 Example Python scripts that use LAMMPS -

    -

    These are the Python scripts included as demos in the python/examples -directory of the LAMMPS distribution, to illustrate the kinds of -things that are possible when Python wraps LAMMPS. If you create your -own scripts, send them to us and we can include them in the LAMMPS -distribution. -

    -
    - - - - - - -
    trivial.py read/run a LAMMPS input script thru Python
    demo.py invoke various LAMMPS library interface routines
    simple.py mimic operation of couple/simple/simple.cpp in Python
    gui.py GUI go/stop/temperature-slider to control LAMMPS
    plot.py real-time temeperature plot with GnuPlot via Pizza.py
    viz_tool.py real-time viz via some viz package
    vizplotgui_tool.py combination of viz_tool.py and plot.py and gui.py -
    - -
    - -

    For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" -with "gl" or "atomeye" or "pymol" or "vmd", depending on what -visualization package you have installed. -

    -

    Note that for GL, you need to be able to run the Pizza.py GL tool, -which is included in the pizza sub-directory. See the Pizza.py doc -pages for more info: -

    - - -

    Note that for AtomEye, you need version 3, and there is a line in the -scripts that specifies the path and name of the executable. See the -AtomEye WWW pages here or here for more details: -

    -
    http://mt.seas.upenn.edu/Archive/Graphics/A
-http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html 
-
    - - - - -

    The latter link is to AtomEye 3 which has the scriping -capability needed by these Python scripts. -

    -

    Note that for PyMol, you need to have built and installed the -open-source version of PyMol in your Python, so that you can import it -from a Python script. See the PyMol WWW pages here or -here for more details: -

    -
    http://www.pymol.org
-http://sourceforge.net/scm/?type=svn&group_id=4546 
-
    - - - - -

    The latter link is to the open-source version. -

    -

    Note that for VMD, you need a fairly current version (1.8.7 works for -me) and there are some lines in the pizza/vmd.py script for 4 PIZZA -variables that have to match the VMD installation on your system. -

    -
    - -

    See the python/README file for instructions on how to run them and the -source code for individual scripts for comments about what they do. -

    -

    Here are screenshots of the vizplotgui_tool.py script in action for -different visualization package options. Click to see larger images: -

    - - - - - - - - - diff --git a/doc/doc2/Section_start.html b/doc/doc2/Section_start.html deleted file mode 100644 index 33d64e0f6d..0000000000 --- a/doc/doc2/Section_start.html +++ /dev/null @@ -1,1940 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
    - - - - - - -
    - -

    2. Getting Started -

    -

    This section describes how to build and run LAMMPS, for both new and -experienced users. -

    -2.1 What's in the LAMMPS distribution
    -2.2 Making LAMMPS
    -2.3 Making LAMMPS with optional packages
    -2.4 Building LAMMPS via the Make.py script
    -2.5 Building LAMMPS as a library
    -2.6 Running LAMMPS
    -2.7 Command-line options
    -2.8 Screen output
    -2.9 Tips for users of previous versions
    - -
    - -
    - -

    2.1 What's in the LAMMPS distribution -

    -

    When you download a LAMMPS tarball you will need to unzip and untar -the downloaded file with the following commands, after placing the -tarball in an appropriate directory. -

    -
    gunzip lammps*.tar.gz 
-tar xvf lammps*.tar 
-
    -

    This will create a LAMMPS directory containing two files and several -sub-directories: -

    -
    - - - - - - - -
    README text file
    LICENSE the GNU General Public License (GPL)
    bench benchmark problems
    doc documentation
    examples simple test problems
    potentials embedded atom method (EAM) potential files
    src source files
    tools pre- and post-processing tools -
    - -

    Note that the download page also has links to download -Windows exectubles and installers, as well as pre-built executables -for a few specific Linux distributions. It also has instructions for -how to download/install LAMMPS for Macs (via Homebrew), and to -download and update LAMMPS from SVN and Git repositories, which gives -you the same files that are in the download tarball. -

    -

    The Windows and Linux executables for serial or parallel only include -certain packages and bug-fixes/upgrades listed on this -page up to a certain date, as -stated on the download page. If you want an executable with -non-included packages or that is more current, then you'll need to -build LAMMPS yourself, as discussed in the next section. -

    -

    Skip to the Running LAMMPS sections for info on how to -launch a LAMMPS Windows executable on a Windows box. -

    -
    - -

    2.2 Making LAMMPS -

    -

    This section has the following sub-sections: -

    - -
    - -Read this first: - -

    If you want to avoid building LAMMPS yourself, read the preceeding -section about options available for downloading and installing -executables. Details are discussed on the download page. -

    -

    Building LAMMPS can be simple or not-so-simple. If all you need are -the default packages installed in LAMMPS, and MPI is already installed -on your machine, or you just want to run LAMMPS in serial, then you -can typically use the Makefile.mpi or Makefile.serial files in -src/MAKE by typing one of these lines (from the src dir): -

    -
    make mpi
-make serial 
-
    -

    Note that on a facility supercomputer, there are often "modules" -loaded in your environment that provide the compilers and MPI you -should use. In this case, the "mpicxx" compile/link command in -Makefile.mpi should just work by accessing those modules. -

    -

    It may be the case that one of the other Makefile.machine files in the -src/MAKE sub-directories is a better match to your system (type "make" -to see a list), you can use it as-is by typing (for example): -

    -
    make stampede 
-
    -

    If any of these builds (with an existing Makefile.machine) works on -your system, then you're done! -

    -

    If you want to do one of the following: -

    -
    • use optional LAMMPS features that require additional libraries -
    • use optional packages that require additional libraries -
    • use optional accelerator packages that require special compiler/linker settings -
    • run on a specialized platform that has its own compilers, settings, or other libs to use -
    -

    then building LAMMPS is more complicated. You may need to find where -auxiliary libraries exist on your machine or install them if they -don't. You may need to build additional libraries that are part of -the LAMMPS package, before building LAMMPS. You may need to edit a -Makefile.machine file to make it compatible with your system. -

    -

    Note that there is a Make.py tool in the src directory that automates -several of these steps, but you still have to know what you are doing. -Section 2.4 below describes the tool. It is a convenient -way to work with installing/un-installing various packages, the -Makefile.machine changes required by some packages, and the auxiliary -libraries some of them use. -

    -

    Please read the following sections carefully. If you are not -comfortable with makefiles, or building codes on a Unix platform, or -running an MPI job on your machine, please find a local expert to help -you. Many compilation, linking, and run problems that users have are -often not really LAMMPS issues - they are peculiar to the user's -system, compilers, libraries, etc. Such questions are better answered -by a local expert. -

    -

    If you have a build problem that you are convinced is a LAMMPS issue -(e.g. the compiler complains about a line of LAMMPS source code), then -please post the issue to the LAMMPS mail -list. -

    -

    If you succeed in building LAMMPS on a new kind of machine, for which -there isn't a similar machine Makefile included in the -src/MAKE/MACHINES directory, then send it to the developers and we can -include it in the LAMMPS distribution. -

    -
    - -Steps to build a LAMMPS executable: - -

    Step 0 -

    -

    The src directory contains the C++ source and header files for LAMMPS. -It also contains a top-level Makefile and a MAKE sub-directory with -low-level Makefile.* files for many systems and machines. See the -src/MAKE/README file for a quick overview of what files are available -and what sub-directories they are in. -

    -

    The src/MAKE dir has a few files that should work as-is on many -platforms. The src/MAKE/OPTIONS dir has more that invoke additional -compiler, MPI, and other setting options commonly used by LAMMPS, to -illustrate their syntax. The src/MAKE/MACHINES dir has many more that -have been tweaked or optimized for specific machines. These files are -all good starting points if you find you need to change them for your -machine. Put any file you edit into the src/MAKE/MINE directory and -it will be never be touched by any LAMMPS updates. -

    -

    >From within the src directory, type "make" or "gmake". You should see -a list of available choices from src/MAKE and all of its -sub-directories. If one of those has the options you want or is the -machine you want, you can type a command like: -

    -
    make mpi
-or
-make serial_icc
-or
-gmake mac 
-
    -

    Note that the corresponding Makefile.machine can exist in src/MAKE or -any of its sub-directories. If a file with the same name appears in -multiple places (not a good idea), the order they are used is as -follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. -This gives preference to a file you have created/edited and put in -src/MAKE/MINE. -

    -

    Note that on a multi-processor or multi-core platform you can launch a -parallel make, by using the "-j" switch with the make command, which -will build LAMMPS more quickly. -

    -

    If you get no errors and an executable like lmp_mpi or lmp_g++_serial -or lmp_mac is produced, then you're done; it's your lucky day. -

    -

    Note that by default only a few of LAMMPS optional packages are -installed. To build LAMMPS with optional packages, see this -section below. -

    -

    Step 1 -

    -

    If Step 0 did not work, you will need to create a low-level Makefile -for your machine, like Makefile.foo. You should make a copy of an -existing Makefile.* in src/MAKE or one of its sub-directories as a -starting point. The only portions of the file you need to edit are -the first line, the "compiler/linker settings" section, and the -"LAMMPS-specific settings" section. When it works, put the edited -file in src/MAKE/MINE and it will not be altered by any future LAMMPS -updates. -

    -

    Step 2 -

    -

    Change the first line of Makefile.foo to list the word "foo" after the -"#", and whatever other options it will set. This is the line you -will see if you just type "make". -

    -

    Step 3 -

    -

    The "compiler/linker settings" section lists compiler and linker -settings for your C++ compiler, including optimization flags. You can -use g++, the open-source GNU compiler, which is available on all Unix -systems. You can also use mpicxx which will typically be available if -MPI is installed on your system, though you should check which actual -compiler it wraps. Vendor compilers often produce faster code. On -boxes with Intel CPUs, we suggest using the Intel icc compiler, which -can be downloaded from Intel's compiler site. -

    - - -

    If building a C++ code on your machine requires additional libraries, -then you should list them as part of the LIB variable. You should -not need to do this if you use mpicxx. -

    -

    The DEPFLAGS setting is what triggers the C++ compiler to create a -dependency list for a source file. This speeds re-compilation when -source (*.cpp) or header (*.h) files are edited. Some compilers do -not support dependency file creation, or may use a different switch -than -D. GNU g++ and Intel icc works with -D. If your compiler can't -create dependency files, then you'll need to create a Makefile.foo -patterned after Makefile.storm, which uses different rules that do not -involve dependency files. Note that when you build LAMMPS for the -first time on a new platform, a long list of *.d files will be printed -out rapidly. This is not an error; it is the Makefile doing its -normal creation of dependencies. -

    -

    Step 4 -

    -

    The "system-specific settings" section has several parts. Note that -if you change any -D setting in this section, you should do a full -re-compile, after typing "make clean" (which will describe different -clean options). -

    -

    The LMP_INC variable is used to include options that turn on ifdefs -within the LAMMPS code. The options that are currently recogized are: -

    -
    • -DLAMMPS_GZIP -
    • -DLAMMPS_JPEG -
    • -DLAMMPS_PNG -
    • -DLAMMPS_FFMPEG -
    • -DLAMMPS_MEMALIGN -
    • -DLAMMPS_XDR -
    • -DLAMMPS_SMALLBIG -
    • -DLAMMPS_BIGBIG -
    • -DLAMMPS_SMALLSMALL -
    • -DLAMMPS_LONGLONG_TO_LONG -
    • -DPACK_ARRAY -
    • -DPACK_POINTER -
    • -DPACK_MEMCPY -
    -

    The read_data and dump commands will read/write gzipped files if you -compile with -DLAMMPS_GZIP. It requires that your machine supports -the "popen()" function in the standard runtime library and that a gzip -executable can be found by LAMMPS during a run. -

    -

    IMPORTANT NOTE: on some clusters with high-speed networks, using the -fork() library calls (required by popen()) can interfere with the fast -communication library and lead to simulations using compressed output -or input to hang or crash. For selected operations, compressed file -I/O is also available using a compression library instead, which are -provided in the COMPRESS package. From more details about compiling -LAMMPS with packages, please see below. -

    -

    If you use -DLAMMPS_JPEG, the dump image command -will be able to write out JPEG image files. For JPEG files, you must -also link LAMMPS with a JPEG library, as described below. If you use --DLAMMPS_PNG, the dump image command will be able to write -out PNG image files. For PNG files, you must also link LAMMPS with a -PNG library, as described below. If neither of those two defines are -used, LAMMPS will only be able to write out uncompressed PPM image -files. -

    -

    If you use -DLAMMPS_FFMPEG, the dump movie command -will be available to support on-the-fly generation of rendered movies -the need to store intermediate image files. It requires that your -machines supports the "popen" function in the standard runtime library -and that an FFmpeg executable can be found by LAMMPS during the run. -

    -

    IMPORTANT NOTE: Similar to the note above, this option can conflict -with high-speed networks, because it uses popen(). -

    -

    Using -DLAMMPS_MEMALIGN= enables the use of the -posix_memalign() call instead of malloc() when large chunks or memory -are allocated by LAMMPS. This can help to make more efficient use of -vector instructions of modern CPUS, since dynamically allocated memory -has to be aligned on larger than default byte boundaries (e.g. 16 -bytes instead of 8 bytes on x86 type platforms) for optimal -performance. -

    -

    If you use -DLAMMPS_XDR, the build will include XDR compatibility -files for doing particle dumps in XTC format. This is only necessary -if your platform does have its own XDR files available. See the -Restrictions section of the dump command for details. -

    -

    Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D- -DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These -settings refer to use of 4-byte (small) vs 8-byte (big) integers -within LAMMPS, as specified in src/lmptype.h. The only reason to use -the BIGBIG setting is to enable simulation of huge molecular systems -(which store bond topology info) with more than 2 billion atoms, or to -track the image flags of moving atoms that wrap around a periodic box -more than 512 times. Normally, the only reason to use SMALLSMALL is -if your machine does not support 64-bit integers, though you can use -SMALLSMALL setting if you are running in serial or on a desktop -machine or small cluster where you will never run large systems or for -long time (more than 2 billion atoms, more than 2 billion timesteps). -See the Additional build tips section below for more -details on these settings. -

    -

    Note that two packages, USER-ATC and USER-CUDA are not currently -compatible with -DLAMMPS_BIGBIG. Also the GPU package requires the -lib/gpu library to be compiled with the same setting, or the link will -fail. -

    -

    The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or -MPI version does not recognize "long long" data types. In this case a -"long" data type is likely already 64-bits, in which case this setting -will convert to that data type. -

    -

    Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY -options can make for faster parallel FFTs (in the PPPM solver) on some -platforms. The -DPACK_ARRAY setting is the default. See the -kspace_style command for info about PPPM. See -Step 6 below for info about building LAMMPS with an FFT library. -

    -

    Step 5 -

    -

    The 3 MPI variables are used to specify an MPI library to build LAMMPS -with. Note that you do not need to set these if you use the MPI -compiler mpicxx for your CC and LINK setting in the section above. -The MPI wrapper knows where to find the needed files. -

    -

    If you want LAMMPS to run in parallel, you must have an MPI library -installed on your platform. If MPI is installed on your system in the -usual place (under /usr/local), you also may not need to specify these -3 variables, assuming /usr/local is in your path. On some large -parallel machines which use "modules" for their compile/link -environements, you may simply need to include the correct module in -your build environment, before building LAMMPS. Or the parallel -machine may have a vendor-provided MPI which the compiler has no -trouble finding. -

    -

    Failing this, these 3 variables can be used to specify where the mpi.h -file (MPI_INC) and the MPI library file (MPI_PATH) are found and the -name of the library file (MPI_LIB). -

    -

    If you are installing MPI yourself, we recommend Argonne's MPICH2 -or OpenMPI. MPICH can be downloaded from the Argonne MPI -site. OpenMPI can -be downloaded from the OpenMPI site. -Other MPI packages should also work. If you are running on a big -parallel platform, your system people or the vendor should have -already installed a version of MPI, which is likely to be faster -than a self-installed MPICH or OpenMPI, so find out how to build -and link with it. If you use MPICH or OpenMPI, you will have to -configure and build it for your platform. The MPI configure script -should have compiler options to enable you to use the same compiler -you are using for the LAMMPS build, which can avoid problems that can -arise when linking LAMMPS to the MPI library. -

    -

    If you just want to run LAMMPS on a single processor, you can use the -dummy MPI library provided in src/STUBS, since you don't need a true -MPI library installed on your system. See src/MAKE/Makefile.serial -for how to specify the 3 MPI variables in this case. You will also -need to build the STUBS library for your platform before making LAMMPS -itself. Note that if you are building with src/MAKE/Makefile.serial, -e.g. by typing "make serial", then the STUBS library is built for you. -

    -

    To build the STUBS library from the src directory, type "make -mpi-stubs", or from the src/STUBS dir, type "make". This should -create a libmpi_stubs.a file suitable for linking to LAMMPS. If the -build fails, you will need to edit the STUBS/Makefile for your -platform. -

    -

    The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime() -that calls gettimeofday() . If your system doesn't support -gettimeofday() , you'll need to insert code to call another timer. -Note that the ANSI-standard function clock() rolls over after an hour -or so, and is therefore insufficient for timing long LAMMPS -simulations. -

    -

    Step 6 -

    -

    The 3 FFT variables allow you to specify an FFT library which LAMMPS -uses (for performing 1d FFTs) when running the particle-particle -particle-mesh (PPPM) option for long-range Coulombics via the -kspace_style command. -

    -

    LAMMPS supports various open-source or vendor-supplied FFT libraries -for this purpose. If you leave these 3 variables blank, LAMMPS will -use the open-source KISS FFT library, which is -included in the LAMMPS distribution. This library is portable to all -platforms and for typical LAMMPS simulations is almost as fast as FFTW -or vendor optimized libraries. If you are not including the KSPACE -package in your build, you can also leave the 3 variables blank. -

    -

    Otherwise, select which kinds of FFTs to use as part of the FFT_INC -setting by a switch of the form -DFFT_XXX. Recommended values for XXX -are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI, -ACML, and T3E. For backward compatability, using -DFFT_FFTW will use -the FFTW2 library. Using -DFFT_NONE will use the KISS library -described above. -

    -

    You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, -so the compiler and linker can find the needed FFT header and library -files. Note that on some large parallel machines which use "modules" -for their compile/link environements, you may simply need to include -the correct module in your build environment. Or the parallel machine -may have a vendor-provided FFT library which the compiler has no -trouble finding. -

    -

    FFTW is a fast, portable library that should also work on any -platform. You can download it from -www.fftw.org. Both the legacy version 2.1.X and -the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3. -Building FFTW for your box should be as simple as ./configure; make. -Note that on some platforms FFTW2 has been pre-installed, and uses -renamed files indicating the precision it was compiled with, -e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can -specify an additional define variable for FFT_INC called -DFFTW_SIZE, -which will select the correct include file. In this case, for FFT_LIB -you must also manually specify the correct library, namely -lsfftw or --ldfftw. -

    -

    The FFT_INC variable also allows for a -DFFT_SINGLE setting that will -use single-precision FFTs with PPPM, which can speed-up long-range -calulations, particularly in parallel or on GPUs. Fourier transform -and related PPPM operations are somewhat insensitive to floating point -truncation errors and thus do not always need to be performed in -double precision. Using the -DFFT_SINGLE setting trades off a little -accuracy for reduced memory use and parallel communication costs for -transposing 3d FFT data. Note that single precision FFTs have only -been tested with the FFTW3, FFTW2, MKL, and KISS FFT options. -

    -

    Step 7 -

    -

    The 3 JPG variables allow you to specify a JPEG and/or PNG library -which LAMMPS uses when writing out JPEG or PNG files via the dump -image command. These can be left blank if you do not -use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step -4, since in that case JPEG/PNG output will be disabled. -

    -

    A standard JPEG library usually goes by the name libjpeg.a or -libjpeg.so and has an associated header file jpeglib.h. Whichever -JPEG library you have on your platform, you'll need to set the -appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the -compiler and linker can find it. -

    -

    A standard PNG library usually goes by the name libpng.a or libpng.so -and has an associated header file png.h. Whichever PNG library you -have on your platform, you'll need to set the appropriate JPG_INC, -JPG_PATH, and JPG_LIB variables, so that the compiler and linker can -find it. -

    -

    As before, if these header and library files are in the usual place on -your machine, you may not need to set these variables. -

    -

    Step 8 -

    -

    Note that by default only a few of LAMMPS optional packages are -installed. To build LAMMPS with optional packages, see this -section below, before proceeding to Step 9. -

    -

    Step 9 -

    -

    That's it. Once you have a correct Makefile.foo, and you have -pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need -to do from the src directory is type something like this: -

    -
    make foo
-or
-gmake foo 
-
    -

    You should get the executable lmp_foo when the build is complete. -

    -
    - -Errors that can occur when making LAMMPS: - -

    IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler -or linker will state very explicitly what the problem is. The error -message should give you a hint as to which of the steps above has -failed, and what you need to do in order to fix it. Building a code -with a Makefile is a very logical process. The compiler and linker -need to find the appropriate files and those files need to be -compatible with LAMMPS source files. When a make fails, there is -usually a very simple reason, which you or a local expert will need to -fix. -

    -

    Here are two non-obvious errors that can occur: -

    -

    (1) If the make command breaks immediately with errors that indicate -it can't find files with a "*" in their names, this can be because -your machine's native make doesn't support wildcard expansion in a -makefile. Try gmake instead of make. If that doesn't work, try using -a -f switch with your make command to use a pre-generated -Makefile.list which explicitly lists all the needed files, e.g. -

    -
    make makelist
-make -f Makefile.list linux
-gmake -f Makefile.list mac 
-
    -

    The first "make" command will create a current Makefile.list with all -the file names in your src dir. The 2nd "make" command (make or -gmake) will use it to build LAMMPS. Note that you should -include/exclude any desired optional packages before using the "make -makelist" command. -

    -

    (2) If you get an error that says something like 'identifier "atoll" -is undefined', then your machine does not support "long long" -integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described -above in Step 4. -

    -
    - -Additional build tips: - -

    (1) Building LAMMPS for multiple platforms. -

    -

    You can make LAMMPS for multiple platforms from the same src -directory. Each target creates its own object sub-directory called -Obj_target where it stores the system-specific *.o files. -

    -

    (2) Cleaning up. -

    -

    Typing "make clean-all" or "make clean-machine" will delete *.o object -files created when LAMMPS is built, for either all builds or for a -particular machine. -

    -

    (3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or --DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL -

    -

    As explained above, any of these 3 settings can be specified on the -LMP_INC line in your low-level src/MAKE/Makefile.foo. -

    -

    The default is -DLAMMPS_SMALLBIG which allows for systems with up to -2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for -atomic systems which do not store bond topology info and thus do not -require atom IDs. If you use atom IDs for atomic systems (which is -the default) or if you use a molecular model, which stores bond -topology info and thus requires atom IDs, the limit is 2^31 atoms -(about 2 billion). This is because the IDs are stored in 32-bit -integers. -

    -

    Likewise, with this setting, the 3 image flags for each atom (see the -dump doc page for a discussion) are stored in a 32-bit -integer, which means the atoms can only wrap around a periodic box (in -each dimension) at most 512 times. If atoms move through the periodic -box more than this many times, the image flags will "roll over", -e.g. from 511 to -512, which can cause diagnostics like the -mean-squared displacement, as calculated by the compute -msd command, to be faulty. -

    -

    To allow for larger atomic systems with atom IDs or larger molecular -systems or larger image flags, compile with -DLAMMPS_BIGBIG. This -stores atom IDs and image flags in 64-bit integers. This enables -atomic or molecular systems with atom IDS of up to 2^63 atoms (about -9e18). And image flags will not "roll over" until they reach 2^20 = -1048576. -

    -

    If your system does not support 8-byte integers, you will need to -compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the -total number of atoms (for atomic or molecular systems) and timesteps -to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512. -

    -

    Note that in src/lmptype.h there are definitions of all these data -types as well as the MPI data types associated with them. The MPI -types need to be consistent with the associated C data types, or else -LAMMPS will generate a run-time error. As far as we know, the -settings defined in src/lmptype.h are portable and work on every -current system. -

    -

    In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to 2^31 atoms per processor -(about 2 billion). This should not normally be a limitation since such -a problem would have a huge per-processor memory footprint due to -neighbor lists and would run very slowly in terms of CPU secs/timestep. -

    -
    - -Building for a Mac: - -

    OS X is BSD Unix, so it should just work. See the -src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files. -

    -
    - -Building for Windows: - -

    The LAMMPS download page has an option to download both a serial and -parallel pre-built Windows executable. See the Running -LAMMPS section for instructions on running these executables -on a Windows box. -

    -

    The pre-built executables hosted on the LAMMPS download -page are built with a subset -of the available packages; see the download page for the list. These -are single executable files. No examples or documentation in -included. You will need to download the full source code package to -obtain those. -

    -

    As an alternative, you can download "daily builds" (and some older -versions) of the installer packages from -rpm.lammps.org/windows.html. -These executables are built with most optional packages and the -download includes documentation, some tools and most examples. -

    -

    If you want a Windows version with specific packages included and -excluded, you can build it yourself. -

    -

    One way to do this is install and use cygwin to build LAMMPS with a -standard unix style make program, just as you would on a Linux box; -see src/MAKE/MACHINES/Makefile.cygwin. -

    -
    - -

    2.3 Making LAMMPS with optional packages -

    -

    This section has the following sub-sections: -

    - -

    Note that the following Section 2.4 describes the Make.py -tool which can be used to install/un-install packages and build the -auxiliary libraries which some of them use. It can also auto-edit a -Makefile.machine to add settings needed by some packages. -

    -
    - -Package basics: - -

    The source code for LAMMPS is structured as a set of core files which -are always included, plus optional packages. Packages are groups of -files that enable a specific set of features. For example, force -fields for molecular systems or granular systems are in packages. -

    -

    You can see the list of all packages by typing "make package" from -within the src directory of the LAMMPS distribution. This also lists -various make commands that can be used to manipulate packages. -

    -

    If you use a command in a LAMMPS input script that is specific to a -particular package, you must have built LAMMPS with that package, else -you will get an error that the style is invalid or the command is -unknown. Every command's doc page specfies if it is part of a -package. You can also type -

    -
    lmp_machine -h 
-
    -

    to run your executable with the optional -h command-line -switch for "help", which will simply list the styles and -commands known to your executable, and immediately exit. -

    -

    There are two kinds of packages in LAMMPS, standard and user packages. -More information about the contents of standard and user packages is -given in Section_packages of the manual. The -difference between standard and user packages is as follows: -

    -

    Standard packages, such as molecule or kspace, are supported by the -LAMMPS developers and are written in a syntax and style consistent -with the rest of LAMMPS. This means we will answer questions about -them, debug and fix them if necessary, and keep them compatible with -future changes to LAMMPS. -

    -

    User packages, such as user-atc or user-omp, have been contributed by -users, and always begin with the user prefix. If they are a single -command (single file), they are typically in the user-misc package. -Otherwise, they are a a set of files grouped together which add a -specific functionality to the code. -

    -

    User packages don't necessarily meet the requirements of the standard -packages. If you have problems using a feature provided in a user -package, you may need to contact the contributor directly to get help. -Information on how to submit additions you make to LAMMPS as single -files or either a standard or user-contributed package are given in -this section of the documentation. -

    -

    Some packages (both standard and user) require additional auxiliary -libraries when building LAMMPS. See more details below. -

    -
    - -Including/excluding packages: - -

    To use (or not use) a package you must include it (or exclude it) -before building LAMMPS. From the src directory, this is typically as -simple as: -

    -
    make yes-colloid
-make g++ 
-
    -

    or -

    -
    make no-manybody
-make g++ 
-
    -

    IMPORTANT NOTE: You should NOT include/exclude packages and build -LAMMPS in a single make command using multiple targets, e.g. make -yes-colloid g++. This is because the make procedure creates a list of -source files that will be out-of-date for the build if the package -configuration changes within the same command. -

    -

    Some packages have individual files that depend on other packages -being included. LAMMPS checks for this and does the right thing. -I.e. individual files are only included if their dependencies are -already included. Likewise, if a package is excluded, other files -dependent on that package are also excluded. -

    -

    If you will never run simulations that use the features in a -particular packages, there is no reason to include it in your build. -For some packages, this will keep you from having to build auxiliary -libraries (see below), and will also produce a smaller executable -which may run a bit faster. -

    -

    When you download a LAMMPS tarball, these packages are pre-installed -in the src directory: KSPACE, MANYBODY,MOLECULE. When you download -LAMMPS source files from the SVN or Git repositories, no packages are -pre-installed. -

    -

    Packages are included or excluded by typing "make yes-name" or "make -no-name", where "name" is the name of the package in lower-case, e.g. -name = kspace for the KSPACE package or name = user-atc for the -USER-ATC package. You can also type "make yes-standard", "make -no-standard", "make yes-std", "make no-std", "make yes-user", "make -no-user", "make yes-all" or "make no-all" to include/exclude various -sets of packages. Type "make package" to see the all of the -package-related make options. -

    -

    IMPORTANT NOTE: Inclusion/exclusion of a package works by simply -moving files back and forth between the main src directory and -sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), -so that the files are seen or not seen when LAMMPS is built. After -you have included or excluded a package, you must re-build LAMMPS. -

    -

    Additional package-related make options exist to help manage LAMMPS -files that exist in both the src directory and in package -sub-directories. You do not normally need to use these commands -unless you are editing LAMMPS files or have downloaded a patch from -the LAMMPS WWW site. -

    -

    Typing "make package-update" or "make pu" will overwrite src files -with files from the package sub-directories if the package has been -included. It should be used after a patch is installed, since patches -only update the files in the package sub-directory, but not the src -files. Typing "make package-overwrite" will overwrite files in the -package sub-directories with src files. -

    -

    Typing "make package-status" or "make ps" will show which packages are -currently included. Of those that are included, it will list files -that are different in the src directory and package sub-directory. -Typing "make package-diff" lists all differences between these files. -Again, type "make package" to see all of the package-related make -options. -

    -
    - -Packages that require extra libraries: - -

    A few of the standard and user packages require additional auxiliary -libraries. Many of them are provided with LAMMPS, in which case they -must be compiled first, before LAMMPS is built, if you wish to include -that package. If you get a LAMMPS build error about a missing -library, this is likely the reason. See the -Section_packages doc page for a list of -packages that have these kinds of auxiliary libraries. -

    -

    The lib directory in the distribution has sub-directories with package -names that correspond to the needed auxiliary libs, e.g. lib/gpu. -Each sub-directory has a README file that gives more details. Code -for most of the auxiliary libraries is included in that directory. -Examples are the USER-ATC and MEAM packages. -

    -

    A few of the lib sub-directories do not include code, but do include -instructions (and sometimes scripts) that automate the process of -downloading the auxiliary library and installing it so LAMMPS can link -to it. Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD -packages. -

    -

    The lib/python directory (for the PYTHON package) contains only a -choice of Makefile.lammps.* files. This is because no auxiliary code -or libraries are needed, only the Python library and other system libs -that should already available on your system. However, the -Makefile.lammps file is needed to tell LAMMPS which libs to use and -where to find them. -

    -

    For libraries with provided code, the sub-directory README file -(e.g. lib/atc/README) has instructions on how to build that library. -Typically this is done by typing something like: -

    -
    make -f Makefile.g++ 
-
    -

    If one of the provided Makefiles is not appropriate for your system -you will need to edit or add one. Note that all the Makefiles have a -setting for EXTRAMAKE at the top that specifies a Makefile.lammps.* -file. -

    -

    If the library build is successful, it will produce 2 files in the lib -directory: -

    -
    libpackage.a
-Makefile.lammps 
-
    -

    The Makefile.lammps file will be a copy of the EXTRAMAKE file setting -specified in the library Makefile.* you used. -

    -

    Note that you must insure that the settings in Makefile.lammps are -appropriate for your system. If they are not, the LAMMPS build will -fail. -

    -

    As explained in the lib/package/README files, the settings in -Makefile.lammps are used to specify additional system libraries and -their locations so that LAMMPS can build with the auxiliary library. -For example, if the MEAM package is used, the auxiliary library -consists of F90 code, built with a Fortran complier. To link that -library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is -built with, typically requires additional Fortran-to-C libraries be -included in the link. Another example are the BLAS and LAPACK -libraries needed to use the USER-ATC or USER-AWPMD packages. -

    -

    For libraries without provided code, the sub-directory README file has -information on where to download the library and how to build it, -e.g. lib/voronoi/README and lib/smd/README. The README files also -describe how you must either (a) create soft links, via the "ln" -command, in those directories to point to where you built or installed -the packages, or (b) check or edit the Makefile.lammps file in the -same directory to provide that information. -

    -

    Some of the sub-directories, e.g. lib/voronoi, also have an install.py -script which can be used to automate the process of -downloading/building/installing the auxiliary library, and setting the -needed soft links. Type "python install.py" for further instructions. -

    -

    As with the sub-directories containing library code, if the soft links -or settings in the lib/package/Makefile.lammps files are not correct, -the LAMMPS build will typically fail. -

    -
    - -Packages that require Makefile.machine settings - -

    A few packages require specific settings in Makefile.machine, to -either build or use the package effectively. These are the -USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what -flags to add or what variables to define are given on the doc pages -that describe each of these accelerator packages in detail: -

    - -

    Here is a brief summary of what Makefile.machine changes are needed. -Note that the Make.py tool, described in the next Section -2.4 can automatically add the needed info to an existing -machine Makefile, using simple command-line arguments. -

    -

    In src/MAKE/OPTIONS see the following Makefiles for examples of the -changes described below: -

    -
    • Makefile.intel_cpu -
    • Makefile.intel_phi -
    • Makefile.kokkos_omp -
    • Makefile.kokkos_cuda -
    • Makefile.kokkos_phi -
    • Makefile.omp -
    -

    For the USER-INTEL package, you have 2 choices when building. You can -build with CPU or Phi support. The latter uses Xeon Phi chips in -"offload" mode. Each of these modes requires additional settings in -your Makefile.machine for CCFLAGS and LINKFLAGS. -

    -

    For CPU mode (if using an Intel compiler): -

    -
    • CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits -
    • LINKFLAGS: add -fopenmp -
    -

    For Phi mode add the following in addition to the CPU mode flags: -

    -
    • CCFLAGS: add -DLMP_INTEL_OFFLOAD and -
    • LINKFLAGS: add -offload -
    -

    And also add this to CCFLAGS: -

    -
    -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" 
-
    -

    For the KOKKOS package, you have 3 choices when building. You can -build with OMP or Cuda or Phi support. Phi support uses Xeon Phi -chips in "native" mode. This can be done by setting the following -variables in your Makefile.machine: -

    -
    • for OMP support, set OMP = yes -
    • for Cuda support, set OMP = yes and CUDA = yes -
    • for Phi support, set OMP = yes and MIC = yes -
    -

    These can also be set as additional arguments to the make command, e.g. -

    -
    make g++ OMP=yes MIC=yes 
-
    -

    Building the KOKKOS package with CUDA support requires a Makefile -machine that uses the NVIDIA "nvcc" compiler, as well as an -appropriate "arch" setting appropriate to the GPU hardware and NVIDIA -software you have on your machine. See -src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine -Makefile. -

    -

    For the USER-OMP package, your Makefile.machine needs additional -settings for CCFLAGS and LINKFLAGS. -

    -
    • CCFLAGS: add -fopenmp and -restrict -
    • LINKFLAGS: add -fopenmp -
    -

    For the OPT package, your Makefile.machine needs an additional -settings for CCFLAGS. -

    -
    • CCFLAGS: add -restrict -
    -
    - -

    2.4 Building LAMMPS via the Make.py tool -

    -

    The src directory includes a Make.py script, written in Python, which -can be used to automate various steps of the build process. It is -particularly useful for working with the accelerator packages, as well -as other packages which require auxiliary libraries to be built. -

    -

    The goal of the Make.py tool is to allow any complex multi-step LAMMPS -build to be performed as a single Make.py command. And you can -archive the commands, so they can be re-invoked later via the -r -(redo) switch. If you find some LAMMPS build procedure that can't be -done in a single Make.py command, let the developers know, and we'll -see if we can augment the tool. -

    -

    You can run Make.py from the src directory by typing either: -

    -
    Make.py -h
-python Make.py -h 
-
    -

    which will give you help info about the tool. For the former to work, -you may need to edit the first line of Make.py to point to your local -Python. And you may need to insure the script is executable: -

    -
    chmod +x Make.py 
-
    -

    Here are examples of build tasks you can perform with Make.py: -

    -
    - - - - - - - -
    Install/uninstall packages Make.py -p no-lib kokkos omp intel
    Build specific auxiliary libs Make.py -a lib-atc lib-meam
    Build libs for all installed packages Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all
    Create a Makefile from scratch with compiler and MPI settings Make.py -m none -cc g++ -mpi mpich -a file
    Augment Makefile.serial with settings for installed packages Make.py -p intel -intel cpu -m serial -a file
    Add JPG and FFTW support to Makefile.mpi Make.py -m mpi -jpg -fft fftw -a file
    Build LAMMPS with a parallel make using Makefile.mpi Make.py -j 16 -m mpi -a exe
    Build LAMMPS and libs it needs using Makefile.serial with accelerator settings Make.py -p gpu intel -intel cpu -a lib-all file serial -
    - -

    The bench and examples directories give Make.py commands that can be -used to build LAMMPS with the various packages and options needed to -run all the benchmark and example input scripts. See these files for -more details: -

    -
    • bench/README -
    • bench/FERMI/README -
    • bench/KEPLER/README -
    • bench/PHI/README -
    • examples/README -
    • examples/accelerate/README -
    • examples/accelerate/make.list -
    -

    All of the Make.py options and syntax help can be accessed by using -the "-h" switch. -

    -

    E.g. typing "Make.py -h" gives -

    -
    Syntax: Make.py switch args ...
-  switches can be listed in any order
-  help switch:
-    -h prints help and syntax for all other specified switches
-  switch for actions:
-    -a lib-all, lib-dir, clean, file, exe or machine
-    list one or more actions, in any order
-    machine is a Makefile.machine suffix, must be last if used
-  one-letter switches:
-    -d (dir), -j (jmake), -m (makefile), -o (output),
-    -p (packages), -r (redo), -s (settings), -v (verbose)
-  switches for libs:
-    -atc, -awpmd, -colvars, -cuda
-    -gpu, -meam, -poems, -qmmm, -reax
-  switches for build and makefile options:
-    -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png 
-
    -

    Using the "-h" switch with other switches and actions gives additional -info on all the other specified switches or actions. The "-h" can be -anywhere in the command-line and the other switches do not need their -arguments. E.g. type "Make.py -h -d -atc -intel" will print: -

    -
    -d dir
-  dir = LAMMPS home dir
-  if -d not specified, working dir must be lammps/src 
-
    -
    -atc make=suffix lammps=suffix2
-  all args are optional and can be in any order
-  make = use Makefile.suffix (def = g++)
-  lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) 
-
    -
    -intel mode
-  mode = cpu or phi (def = cpu)
-    build Intel package for CPU or Xeon Phi 
-
    -

    Note that Make.py never overwrites an existing Makefile.machine. -Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or -rename if desired. Likewise it creates an executable named -src/lmp_auto, which you can rename using the -o switch if desired. -

    -

    The most recently executed Make.py commmand is saved in -src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke -the last command, or you can save a sequence of one or more Make.py -commands to a file and invoke the file of commands using "-r". You -can also label the commands in the file and invoke one or more of them -by name. -

    -

    A typical use of Make.py is to start with a valid Makefile.machine for -your system, that works for a vanilla LAMMPS build, i.e. when optional -packages are not installed. You can then use Make.py to add various -settings (FFT, JPG, PNG) to the Makefile.machine as well as change its -compiler and MPI options. You can also add additional packages to the -build, as well as build the needed supporting libraries. -

    -

    You can also use Make.py to create a new Makefile.machine from -scratch, using the "-m none" switch, if you also specify what compiler -and MPI options to use, via the "-cc" and "-mpi" switches. -

    -
    - -

    2.5 Building LAMMPS as a library -

    -

    LAMMPS can be built as either a static or shared library, which can -then be called from another application or a scripting language. See -this section for more info on coupling -LAMMPS to other codes. See this section for -more info on wrapping and running LAMMPS from Python. -

    -
    Static library: -
    -

    To build LAMMPS as a static library (*.a file on Linux), type -

    -
    make foo mode=lib 
-
    -

    where foo is the machine name. This kind of library is typically used -to statically link a driver application to LAMMPS, so that you can -insure all dependencies are satisfied at compile time. This will use -the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build -will create the file liblammps_foo.a which another application can -link to. It will also create a soft link liblammps.a, which will -point to the most recently built static library. -

    -
    Shared library: -
    -

    To build LAMMPS as a shared library (*.so file on Linux), which can be -dynamically loaded, e.g. from Python, type -

    -
    make foo mode=shlib 
-
    -

    where foo is the machine name. This kind of library is required when -wrapping LAMMPS with Python; see Section_python -for details. This will use the SHFLAGS and SHLIBFLAGS settings in -src/MAKE/Makefile.foo and perform the build in the directory -Obj_shared_foo. This is so that each file can be compiled with the --fPIC flag which is required for inclusion in a shared library. The -build will create the file liblammps_foo.so which another application -can link to dyamically. It will also create a soft link liblammps.so, -which will point to the most recently built shared library. This is -the file the Python wrapper loads by default. -

    -

    Note that for a shared library to be usable by a calling program, all -the auxiliary libraries it depends on must also exist as shared -libraries. This will be the case for libraries included with LAMMPS, -such as the dummy MPI library in src/STUBS or any package libraries in -lib/packages, since they are always built as shared libraries using -the -fPIC switch. However, if a library like MPI or FFTW does not -exist as a shared library, the shared library build will generate an -error. This means you will need to install a shared library version -of the auxiliary library. The build instructions for the library -should tell you how to do this. -

    -

    Here is an example of such errors when the system FFTW or provided -lib/colvars library have not been built as shared libraries: -

    -
    /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
-R_X86_64_32 against `.rodata' can not be used when making a shared
-object; recompile with -fPIC
-/usr/local/lib/libfftw3.a: could not read symbols: Bad value 
-
    -
    /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
-relocation R_X86_64_32 against `__pthread_key_create' can not be used
-when making a shared object; recompile with -fPIC
-../../lib/colvars/libcolvars.a: error adding symbols: Bad value 
-
    -

    As an example, here is how to build and install the MPICH -library, a popular open-source version of MPI, distributed by -Argonne National Labs, as a shared library in the default -/usr/local/lib location: -

    - - -
    ./configure --enable-shared
-make
-make install 
-
    -

    You may need to use "sudo make install" in place of the last line if -you do not have write privileges for /usr/local/lib. The end result -should be the file /usr/local/lib/libmpich.so. -

    -
    Additional requirement for using a shared library: -
    -

    The operating system finds shared libraries to load at run-time using -the environment variable LD_LIBRARY_PATH. So you may wish to copy the -file src/liblammps.so or src/liblammps_g++.so (for example) to a place -the system can find it by default, such as /usr/local/lib, or you may -wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the -current version of the shared library is always available to programs -that use it. -

    -

    For the csh or tcsh shells, you would add something like this to your -~/.cshrc file: -

    -
    setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src 
-
    -
    Calling the LAMMPS library: -
    -

    Either flavor of library (static or shared) allows one or more LAMMPS -objects to be instantiated from the calling program. -

    -

    When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS -namespace; you can safely use any of its classes and methods from -within the calling code, as needed. -

    -

    When used from a C or Fortran program or a scripting language like -Python, the library has a simple function-style interface, provided in -src/library.cpp and src/library.h. -

    -

    See the sample codes in examples/COUPLE/simple for examples of C++ and -C and Fortran codes that invoke LAMMPS thru its library interface. -There are other examples as well in the COUPLE directory which are -discussed in Section_howto 10 of the -manual. See Section_python of the manual for a -description of the Python wrapper provided with LAMMPS that operates -through the LAMMPS library interface. -

    -

    The files src/library.cpp and library.h define the C-style API for -using LAMMPS as a library. See Section_howto -19 of the manual for a description of the -interface and how to extend it for your needs. -

    -
    - -

    2.6 Running LAMMPS -

    -

    By default, LAMMPS runs by reading commands from standard input. Thus -if you run the LAMMPS executable by itself, e.g. -

    -
    lmp_linux 
-
    -

    it will simply wait, expecting commands from the keyboard. Typically -you should put commands in an input script and use I/O redirection, -e.g. -

    -
    lmp_linux < in.file 
-
    -

    For parallel environments this should also work. If it does not, use -the '-in' command-line switch, e.g. -

    -
    lmp_linux -in in.file 
-
    -

    This section describes how input scripts are -structured and what commands they contain. -

    -

    You can test LAMMPS on any of the sample inputs provided in the -examples or bench directory. Input scripts are named in.* and sample -outputs are named log.*.name.P where name is a machine and P is the -number of processors it was run on. -

    -

    Here is how you might run a standard Lennard-Jones benchmark on a -Linux box, using mpirun to launch a parallel job: -

    -
    cd src
-make linux
-cp lmp_linux ../bench
-cd ../bench
-mpirun -np 4 lmp_linux -in in.lj 
-
    -

    See this page for timings for this and the other benchmarks on -various platforms. Note that some of the example scripts require -LAMMPS to be built with one or more of its optional packages. -

    - - -
    - -

    On a Windows box, you can skip making LAMMPS and simply download an -executable, as described above, though the pre-packaged executables -include only certain packages. -

    -

    To run a LAMMPS executable on a Windows machine, first decide whether -you want to download the non-MPI (serial) or the MPI (parallel) -version of the executable. Download and save the version you have -chosen. -

    -

    For the non-MPI version, follow these steps: -

    -
    • Get a command prompt by going to Start->Run... , -then typing "cmd". - -
    • Move to the directory where you have saved lmp_win_no-mpi.exe -(e.g. by typing: cd "Documents"). - -
    • At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj -with the name of your LAMMPS input script. -
    -

    For the MPI version, which allows you to run LAMMPS under Windows on -multiple processors, follow these steps: -

    -
    • Download and install -MPICH2 -for Windows. - -
    • You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 -package. Put them in same directory (or path) as the LAMMPS Windows -executable. - -
    • Get a command prompt by going to Start->Run... , -then typing "cmd". - -
    • Move to the directory where you have saved lmp_win_mpi.exe -(e.g. by typing: cd "Documents"). - -
    • Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in -in.lj", replacing in.lj with the name of your LAMMPS input script. - -
    • Note that you may need to provide smpd with a passphrase (it doesn't -matter what you type). - -
    • In this mode, output may not immediately show up on the screen, so if -your input script takes a long time to execute, you may need to be -patient before the output shows up. :l Alternatively, you can still -use this executable to run on a single processor by typing something -like: "lmp_win_mpi -in in.lj". -
    -
    - -

    The screen output from LAMMPS is described in the next section. As it -runs, LAMMPS also writes a log.lammps file with the same information. -

    -

    Note that this sequence of commands copies the LAMMPS executable -(lmp_linux) to the directory with the input files. This may not be -necessary, but some versions of MPI reset the working directory to -where the executable is, rather than leave it as the directory where -you launch mpirun from (if you launch lmp_linux on its own and not -under mpirun). If that happens, LAMMPS will look for additional input -files and write its output files to the executable directory, rather -than your working directory, which is probably not what you want. -

    -

    If LAMMPS encounters errors in the input script or while running a -simulation it will print an ERROR message and stop or a WARNING -message and continue. See Section_errors for a -discussion of the various kinds of errors LAMMPS can or can't detect, -a list of all ERROR and WARNING messages, and what to do about them. -

    -

    LAMMPS can run a problem on any number of processors, including a -single processor. In theory you should get identical answers on any -number of processors and on any machine. In practice, numerical -round-off can cause slight differences and eventual divergence of -molecular dynamics phase space trajectories. -

    -

    LAMMPS can run as large a problem as will fit in the physical memory -of one or more processors. If you run out of memory, you must run on -more processors or setup a smaller problem. -

    -
    - -

    2.7 Command-line options -

    -

    At run time, LAMMPS recognizes several optional command-line switches -which may be used in any order. Either the full word or a one-or-two -letter abbreviation can be used: -

    -
    • -c or -cuda -
    • -e or -echo -
    • -h or -help -
    • -i or -in -
    • -k or -kokkos -
    • -l or -log -
    • -nc or -nocite -
    • -pk or -package -
    • -p or -partition -
    • -pl or -plog -
    • -ps or -pscreen -
    • -r or -restart -
    • -ro or -reorder -
    • -sc or -screen -
    • -sf or -suffix -
    • -v or -var -
    -

    For example, lmp_ibm might be launched as follows: -

    -
    mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
-mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy 
-
    -

    Here are the details on the options: -

    -
    -cuda on/off 
-
    -

    Explicitly enable or disable CUDA support, as provided by the -USER-CUDA package. Even if LAMMPS is built with this package, as -described above in Section 2.3, this switch must be set to -enable running with the CUDA-enabled styles the package provides. If -the switch is not set (the default), LAMMPS will operate as if the -USER-CUDA package were not installed; i.e. you can run standard LAMMPS -or with the GPU package, for testing or benchmarking purposes. -

    -
    -echo style 
-
    -

    Set the style of command echoing. The style can be none or screen -or log or both. Depending on the style, each command read from -the input script will be echoed to the screen and/or logfile. This -can be useful to figure out which line of your script is causing an -input error. The default value is log. The echo style can also be -set by using the echo command in the input script itself. -

    -
    -help 
-
    -

    Print a brief help summary and a list of options compiled into this -executable for each LAMMPS style (atom_style, fix, compute, -pair_style, bond_style, etc). This can tell you if the command you -want to use was included via the appropriate package at compile time. -LAMMPS will print the info and immediately exit if this switch is -used. -

    -
    -in file 
-
    -

    Specify a file to use as an input script. This is an optional switch -when running LAMMPS in one-partition mode. If it is not specified, -LAMMPS reads its script from standard input, typically from a script -via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should -also work in parallel, but if it does not (in the unlikely case that -an MPI implementation does not support it), then use the -in flag. -Note that this is a required switch when running LAMMPS in -multi-partition mode, since multiple processors cannot all read from -stdin. -

    -
    -kokkos on/off keyword/value ... 
-
    -

    Explicitly enable or disable KOKKOS support, as provided by the KOKKOS -package. Even if LAMMPS is built with this package, as described -above in Section 2.3, this switch must be set to enable -running with the KOKKOS-enabled styles the package provides. If the -switch is not set (the default), LAMMPS will operate as if the KOKKOS -package were not installed; i.e. you can run standard LAMMPS or with -the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking -purposes. -

    -

    Additional optional keyword/value pairs can be specified which -determine how Kokkos will use the underlying hardware on your -platform. These settings apply to each MPI task you launch via the -"mpirun" or "mpiexec" command. You may choose to run one or more MPI -tasks per physical node. Note that if you are running on a desktop -machine, you typically have one physical node. On a cluster or -supercomputer there may be dozens or 1000s of physical nodes. -

    -

    Either the full word or an abbreviation can be used for the keywords. -Note that the keywords do not use a leading minus sign. I.e. the -keyword is "t", not "-t". Also note that each of the keywords has a -default setting. Example of when to use these options and what -settings to use on different platforms is given in Section -5.8. -

    -
    • d or device -
    • g or gpus -
    • t or threads -
    • n or numa -
    -
    device Nd 
-
    -

    This option is only relevant if you built LAMMPS with CUDA=yes, you -have more than one GPU per node, and if you are running with only one -MPI task per node. The Nd setting is the ID of the GPU on the node to -run on. By default Nd = 0. If you have multiple GPUs per node, they -have consecutive IDs numbered as 0,1,2,etc. This setting allows you -to launch multiple independent jobs on the node, each with a single -MPI task per node, and assign each job to run on a different GPU. -

    -
    gpus Ng Ns 
-
    -

    This option is only relevant if you built LAMMPS with CUDA=yes, you -have more than one GPU per node, and you are running with multiple MPI -tasks per node (up to one per GPU). The Ng setting is how many GPUs -you will use. The Ns setting is optional. If set, it is the ID of a -GPU to skip when assigning MPI tasks to GPUs. This may be useful if -your desktop system reserves one GPU to drive the screen and the rest -are intended for computational work like running LAMMPS. By default -Ng = 1 and Ns is not set. -

    -

    Depending on which flavor of MPI you are running, LAMMPS will look for -one of these 3 environment variables -

    -
    SLURM_LOCALID (various MPI variants compiled with SLURM support)
-MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
-OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) 
-
    -

    which are initialized by the "srun", "mpirun" or "mpiexec" commands. -The environment variable setting for each MPI rank is used to assign a -unique GPU ID to the MPI task. -

    -
    threads Nt 
-
    -

    This option assigns Nt number of threads to each MPI task for -performing work when Kokkos is executing in OpenMP or pthreads mode. -The default is Nt = 1, which essentially runs in MPI-only mode. If -there are Np MPI tasks per physical node, you generally want Np*Nt = -the number of physical cores per node, to use your available hardware -optimally. This also sets the number of threads used by the host when -LAMMPS is compiled with CUDA=yes. -

    -
    numa Nm 
-
    -

    This option is only relevant when using pthreads with hwloc support. -In this case Nm defines the number of NUMA regions (typicaly sockets) -on a node which will be utilizied by a single MPI rank. By default Nm -= 1. If this option is used the total number of worker-threads per -MPI rank is threads*numa. Currently it is always almost better to -assign at least one MPI rank per NUMA region, and leave numa set to -its default value of 1. This is because letting a single process span -multiple NUMA regions induces a significant amount of cross NUMA data -traffic which is slow. -

    -
    -log file 
-
    -

    Specify a log file for LAMMPS to write status information to. In -one-partition mode, if the switch is not used, LAMMPS writes to the -file log.lammps. If this switch is used, LAMMPS writes to the -specified file. In multi-partition mode, if the switch is not used, a -log.lammps file is created with hi-level status information. Each -partition also writes to a log.lammps.N file where N is the partition -ID. If the switch is specified in multi-partition mode, the hi-level -logfile is named "file" and each partition also logs information to a -file.N. For both one-partition and multi-partition mode, if the -specified file is "none", then no log files are created. Using a -log command in the input script will override this setting. -Option -plog will override the name of the partition log files file.N. -

    -
    -nocite 
-
    -

    Disable writing the log.cite file which is normally written to list -references for specific cite-able features used during a LAMMPS run. -See the citation page for more -details. -

    -
    -package style args .... 
-
    -

    Invoke the package command with style and args. The -syntax is the same as if the command appeared at the top of the input -script. For example "-package gpu 2" or "-pk gpu 2" is the same as -package gpu 2 in the input script. The possible styles -and args are documented on the package doc page. This -switch can be used multiple times, e.g. to set options for the -USER-INTEL and USER-OMP packages which can be used together. -

    -

    Along with the "-suffix" command-line switch, this is a convenient -mechanism for invoking accelerator packages and their options without -having to edit an input script. -

    -
    -partition 8x2 4 5 ... 
-
    -

    Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P -processors and this switch is not used, LAMMPS runs in one partition, -i.e. all P processors run a single simulation. If this switch is -used, the P processors are split into separate partitions and each -partition runs its own simulation. The arguments to the switch -specify the number of processors in each partition. Arguments of the -form MxN mean M partitions, each with N processors. Arguments of the -form N mean a single partition with N processors. The sum of -processors in all partitions must equal P. Thus the command -"-partition 8x2 4 5" has 10 partitions and runs on a total of 25 -processors. -

    -

    Running with multiple partitions can e useful for running -multi-replica simulations, where each -replica runs on on one or a few processors. Note that with MPI -installed on a machine (e.g. your desktop), you can run on more -(virtual) processors than you have physical processors. -

    -

    To run multiple independent simulatoins from one input script, using -multiple partitions, see Section_howto 4 -of the manual. World- and universe-style variables -are useful in this context. -

    -
    -plog file 
-
    -

    Specify the base name for the partition log files, so partition N -writes log information to file.N. If file is none, then no partition -log files are created. This overrides the filename specified in the --log command-line option. This option is useful when working with -large numbers of partitions, allowing the partition log files to be -suppressed (-plog none) or placed in a sub-directory (-plog -replica_files/log.lammps) If this option is not used the log file for -partition N is log.lammps.N or whatever is specified by the -log -command-line option. -

    -
    -pscreen file 
-
    -

    Specify the base name for the partition screen file, so partition N -writes screen information to file.N. If file is none, then no -partition screen files are created. This overrides the filename -specified in the -screen command-line option. This option is useful -when working with large numbers of partitions, allowing the partition -screen files to be suppressed (-pscreen none) or placed in a -sub-directory (-pscreen replica_files/screen). If this option is not -used the screen file for partition N is screen.N or whatever is -specified by the -screen command-line option. -

    -
    -restart restartfile remap datafile keyword value ... 
-
    -

    Convert the restart file into a data file and immediately exit. This -is the same operation as if the following 2-line input script were -run: -

    -
    read_restart restartfile remap
-write_data datafile keyword value ... 
-
    -

    Note that the specified restartfile and datafile can have wild-card -characters ("*",%") as described by the -read_restart and write_data -commands. But a filename such as file.* will need to be enclosed in -quotes to avoid shell expansion of the "*" character. -

    -

    Note that following restartfile, the optional flag remap can be -used. This has the same effect as adding it to the -read_restart command, as explained on its doc -page. This is only useful if the reading of the restart file triggers -an error that atoms have been lost. In that case, use of the remap -flag should allow the data file to still be produced. -

    -

    Also note that following datafile, the same optional keyword/value -pairs can be listed as used by the write_data -command. -

    -
    -reorder nth N
--reorder custom filename 
-
    -

    Reorder the processors in the MPI communicator used to instantiate -LAMMPS, in one of several ways. The original MPI communicator ranks -all P processors from 0 to P-1. The mapping of these ranks to -physical processors is done by MPI before LAMMPS begins. It may be -useful in some cases to alter the rank order. E.g. to insure that -cores within each node are ranked in a desired order. Or when using -the run_style verlet/split command with 2 partitions -to insure that a specific Kspace processor (in the 2nd partition) is -matched up with a specific set of processors in the 1st partition. -See the Section_accelerate doc pages for -more details. -

    -

    If the keyword nth is used with a setting N, then it means every -Nth processor will be moved to the end of the ranking. This is useful -when using the run_style verlet/split command with 2 -partitions via the -partition command-line switch. The first set of -processors will be in the first partition, the 2nd set in the 2nd -partition. The -reorder command-line switch can alter this so that -the 1st N procs in the 1st partition and one proc in the 2nd partition -will be ordered consecutively, e.g. as the cores on one physical node. -This can boost performance. For example, if you use "-reorder nth 4" -and "-partition 9 3" and you are running on 12 processors, the -processors will be reordered from -

    -
    0 1 2 3 4 5 6 7 8 9 10 11 
-
    -

    to -

    -
    0 1 2 4 5 6 8 9 10 3 7 11 
-
    -

    so that the processors in each partition will be -

    -
    0 1 2 4 5 6 8 9 10 
-3 7 11 
-
    -

    See the "processors" command for how to insure processors from each -partition could then be grouped optimally for quad-core nodes. -

    -

    If the keyword is custom, then a file that specifies a permutation -of the processor ranks is also specified. The format of the reorder -file is as follows. Any number of initial blank or comment lines -(starting with a "#" character) can be present. These should be -followed by P lines of the form: -

    -
    I J 
-
    -

    where P is the number of processors LAMMPS was launched with. Note -that if running in multi-partition mode (see the -partition switch -above) P is the total number of processors in all partitions. The I -and J values describe a permutation of the P processors. Every I and -J should be values from 0 to P-1 inclusive. In the set of P I values, -every proc ID should appear exactly once. Ditto for the set of P J -values. A single I,J pairing means that the physical processor with -rank I in the original MPI communicator will have rank J in the -reordered communicator. -

    -

    Note that rank ordering can also be specified by many MPI -implementations, either by environment variables that specify how to -order physical processors, or by config files that specify what -physical processors to assign to each MPI rank. The -reorder switch -simply gives you a portable way to do this without relying on MPI -itself. See the processors out command for how to output -info on the final assignment of physical processors to the LAMMPS -simulation domain. -

    -
    -screen file 
-
    -

    Specify a file for LAMMPS to write its screen information to. In -one-partition mode, if the switch is not used, LAMMPS writes to the -screen. If this switch is used, LAMMPS writes to the specified file -instead and you will see no screen output. In multi-partition mode, -if the switch is not used, hi-level status information is written to -the screen. Each partition also writes to a screen.N file where N is -the partition ID. If the switch is specified in multi-partition mode, -the hi-level screen dump is named "file" and each partition also -writes screen information to a file.N. For both one-partition and -multi-partition mode, if the specified file is "none", then no screen -output is performed. Option -pscreen will override the name of the -partition screen files file.N. -

    -
    -suffix style args 
-
    -

    Use variants of various styles if they exist. The specified style can -be cuda, gpu, intel, kk, omp, opt, or hybrid. These refer -to optional packages that LAMMPS can be built with, as described above in -Section 2.3. The "cuda" style corresponds to the USER-CUDA -package, the "gpu" style to the GPU package, the "intel" style to the -USER-INTEL package, the "kk" style to the KOKKOS package, the "opt" -style to the OPT package, and the "omp" style to the USER-OMP package. The -hybrid style is the only style that accepts arguments. It allows for two -packages to be specified. The first package specified is the default and -will be used if it is available. If no style is available for the first -package, the style for the second package will be used if available. For -example, "-suffix hybrid intel omp" will use styles from the USER-INTEL -package if they are installed and available, but styles for the USER-OMP -package otherwise. -

    -

    Along with the "-package" command-line switch, this is a convenient -mechanism for invoking accelerator packages and their options without -having to edit an input script. -

    -

    As an example, all of the packages provide a pair_style -lj/cut variant, with style names lj/cut/cuda, -lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A -variant style can be specified explicitly in your input script, -e.g. pair_style lj/cut/gpu. If the -suffix switch is used the -specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended -whenever your input script command creates a new -atom, pair, fix, -compute, or run style. If the variant -version does not exist, the standard version is created. -

    -

    For the GPU package, using this command-line switch also invokes the -default GPU settings, as if the command "package gpu 1" were used at -the top of your input script. These settings can be changed by using -the "-package gpu" command-line switch or the package -gpu command in your script. -

    -

    For the USER-INTEL package, using this command-line switch also -invokes the default USER-INTEL settings, as if the command "package -intel 1" were used at the top of your input script. These settings -can be changed by using the "-package intel" command-line switch or -the package intel command in your script. If the -USER-OMP package is also installed, the hybrid style with "intel omp" -arguments can be used to make the omp suffix a second choice, if a -requested style is not available in the USER-INTEL package. It will -also invoke the default USER-OMP settings, as if the command "package -omp 0" were used at the top of your input script. These settings can -be changed by using the "-package omp" command-line switch or the -package omp command in your script. -

    -

    For the KOKKOS package, using this command-line switch also invokes -the default KOKKOS settings, as if the command "package kokkos" were -used at the top of your input script. These settings can be changed -by using the "-package kokkos" command-line switch or the package -kokkos command in your script. -

    -

    For the OMP package, using this command-line switch also invokes the -default OMP settings, as if the command "package omp 0" were used at -the top of your input script. These settings can be changed by using -the "-package omp" command-line switch or the package -omp command in your script. -

    -

    The suffix command can also be used within an input -script to set a suffix, or to turn off or back on any suffix setting -made via the command line. -

    -
    -var name value1 value2 ... 
-
    -

    Specify a variable that will be defined for substitution purposes when -the input script is read. This switch can be used multiple times to -define multiple variables. "Name" is the variable name which can be a -single character (referenced as $x in the input script) or a full -string (referenced as ${abc}). An index-style -variable will be created and populated with the -subsequent values, e.g. a set of filenames. Using this command-line -option is equivalent to putting the line "variable name index value1 -value2 ..." at the beginning of the input script. Defining an index -variable as a command-line argument overrides any setting for the same -index variable in the input script, since index variables cannot be -re-defined. See the variable command for more info on -defining index and other kinds of variables and this -section for more info on using variables -in input scripts. -

    -

    NOTE: Currently, the command-line parser looks for arguments that -start with "-" to indicate new switches. Thus you cannot specify -multiple variable values if any of they start with a "-", e.g. a -negative numeric value. It is OK if the first value1 starts with a -"-", since it is automatically skipped. -

    -
    - -

    2.8 LAMMPS screen output -

    -

    As LAMMPS reads an input script, it prints information to both the -screen and a log file about significant actions it takes to setup a -simulation. When the simulation is ready to begin, LAMMPS performs -various initializations and prints the amount of memory (in MBytes per -processor) that the simulation requires. It also prints details of -the initial thermodynamic state of the system. During the run itself, -thermodynamic information is printed periodically, every few -timesteps. When the run concludes, LAMMPS prints the final -thermodynamic state and a total run time for the simulation. It then -appends statistics about the CPU time and storage requirements for the -simulation. An example set of statistics is shown here: -

    -

    Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms -

    -
    Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
-97.0% CPU use with 4 MPI tasks x no OpenMP threads 
-
    -
    MPI task timings breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.9808     | 2.0134     | 2.0318     |   1.4 | 71.60
-Bond    | 0.0021894  | 0.0060319  | 0.010058   |   4.7 |  0.21
-Kspace  | 0.3207     | 0.3366     | 0.36616    |   3.1 | 11.97
-Neigh   | 0.28411    | 0.28464    | 0.28516    |   0.1 | 10.12
-Comm    | 0.075732   | 0.077018   | 0.07883    |   0.4 |  2.74
-Output  | 0.00030518 | 0.00042665 | 0.00078821 |   1.0 |  0.02
-Modify  | 0.086606   | 0.086631   | 0.086668   |   0.0 |  3.08
-Other   |            | 0.007178   |            |       |  0.26 
-
    -
    Nlocal:    501 ave 508 max 490 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-Nghost:    6586.25 ave 6628 max 6548 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs:    177007 ave 180562 max 170212 min
-Histogram: 1 0 0 0 0 0 0 1 1 1 
-
    -
    Total # of neighbors = 708028
-Ave neighs/atom = 353.307
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 26
-Dangerous builds = 0 
-
    -

    The first section provides a global loop timing summary. The loop time -is the total wall time for the section. The Performance line is -provided for convenience to help predicting the number of loop -continuations required and for comparing performance with other -similar MD codes. The CPU use line provides the CPU utilzation per -MPI task; it should be close to 100% times the number of OpenMP -threads (or 1). Lower numbers correspond to delays due to file I/O or -insufficient thread utilization. -

    -

    The MPI task section gives the breakdown of the CPU run time (in -seconds) into major categories: -

    -
    • Pair stands for all non-bonded force computation -
    • Bond stands for bonded interactions: bonds, angles, dihedrals, impropers -
    • Kspace stands for reciprocal space interactions: Ewald, PPPM, MSM -
    • Neigh stands for neighbor list construction -
    • Comm stands for communicating atoms and their properties -
    • Output stands for writing dumps and thermo output -
    • Modify stands for fixes and computes called by them -
    • Other is the remaining time -
    -

    For each category, there is a breakdown of the least, average and most -amount of wall time a processor spent on this section. Also you have the -variation from the average time. Together these numbers allow to gauge -the amount of load imbalance in this segment of the calculation. Ideally -the difference between minimum, maximum and average is small and thus -the variation from the average close to zero. The final column shows -the percentage of the total loop time is spent in this section. -

    -

    When using the timer full setting, an additional column -is present that also prints the CPU utilization in percent. In -addition, when using timer full and the package omp -command are active, a similar timing summary of time spent in threaded -regions to monitor thread utilization and load balance is provided. A -new entry is the Reduce section, which lists the time spend in -reducing the per-thread data elements to the storage for non-threaded -computation. These thread timings are taking from the first MPI rank -only and and thus, as the breakdown for MPI tasks can change from MPI -rank to MPI rank, this breakdown can be very different for individual -ranks. Here is an example output for this section: -

    -

    Thread timings breakdown (MPI rank 0): -Total threaded time 0.6846 / 90.6% -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18 -Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68 -Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89 -Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70 -Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 -

    -

    The third section lists the number of owned atoms (Nlocal), ghost atoms -(Nghost), and pair-wise neighbors stored per processor. The max and min -values give the spread of these values across processors with a 10-bin -histogram showing the distribution. The total number of histogram counts -is equal to the number of processors. -

    -

    The last section gives aggregate statistics for pair-wise neighbors -and special neighbors that LAMMPS keeps track of (see the -special_bonds command). The number of times -neighbor lists were rebuilt during the run is given as well as the -number of potentially "dangerous" rebuilds. If atom movement -triggered neighbor list rebuilding (see the -neigh_modify command), then dangerous -reneighborings are those that were triggered on the first timestep -atom movement was checked for. If this count is non-zero you may wish -to reduce the delay factor to insure no force interactions are missed -by atoms moving beyond the neighbor skin distance before a rebuild -takes place. -

    -

    If an energy minimization was performed via the -minimize command, additional information is printed, -e.g. -

    -
    Minimization stats:
-  Stopping criterion = linesearch alpha is zero
-  Energy initial, next-to-last, final = 
-         -6372.3765206     -8328.46998942     -8328.46998942
-  Force two-norm initial, final = 1059.36 5.36874
-  Force max component initial, final = 58.6026 1.46872
-  Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
-  Iterations, force evaluations = 701 1516 
-
    -

    The first line prints the criterion that determined the minimization -to be completed. The third line lists the initial and final energy, -as well as the energy on the next-to-last iteration. The next 2 lines -give a measure of the gradient of the energy (force on all atoms). -The 2-norm is the "length" of this force vector; the inf-norm is the -largest component. Then some information about the line search and -statistics on how many iterations and force-evaluations the minimizer -required. Multiple force evaluations are typically done at each -iteration to perform a 1d line minimization in the search direction. -

    -

    If a kspace_style long-range Coulombics solve was -performed during the run (PPPM, Ewald), then additional information is -printed, e.g. -

    -
    FFT time (% of Kspce) = 0.200313 (8.34477)
-FFT Gflps 3d 1d-only = 2.31074 9.19989 
-
    -

    The first line gives the time spent doing 3d FFTs (4 per timestep) and -the fraction it represents of the total KSpace time (listed above). -Each 3d FFT requires computation (3 sets of 1d FFTs) and communication -(transposes). The total flops performed is 5Nlog_2(N), where N is the -number of points in the 3d grid. The FFTs are timed with and without -the communication and a Gflop rate is computed. The 3d rate is with -communication; the 1d rate is without (just the 1d FFTs). Thus you -can estimate what fraction of your FFT time was spent in -communication, roughly 75% in the example above. -

    -
    - -

    2.9 Tips for users of previous LAMMPS versions -

    -

    The current C++ began with a complete rewrite of LAMMPS 2001, which -was written in F90. Features of earlier versions of LAMMPS are listed -in Section_history. The F90 and F77 versions -(2001 and 99) are also freely distributed as open-source codes; check -the LAMMPS WWW Site for distribution information if you prefer -those versions. The 99 and 2001 versions are no longer under active -development; they do not have all the features of C++ LAMMPS. -

    -

    If you are a previous user of LAMMPS 2001, these are the most -significant changes you will notice in C++ LAMMPS: -

    -

    (1) The names and arguments of many input script commands have -changed. All commands are now a single word (e.g. read_data instead -of read data). -

    -

    (2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS, -but you may need to specify the relevant commands in different ways. -

    -

    (3) The format of the data file can be streamlined for some problems. -See the read_data command for details. The data file -section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS. -

    -

    (4) Binary restart files written by LAMMPS 2001 cannot be read by C++ -LAMMPS with a read_restart command. This is -because they were output by F90 which writes in a different binary -format than C or C++ writes or reads. Use the restart2data tool -provided with LAMMPS 2001 to convert the 2001 restart file to a text -data file. Then edit the data file as necessary before using the C++ -LAMMPS read_data command to read it in. -

    -

    (5) There are numerous small numerical changes in C++ LAMMPS that mean -you will not get identical answers when comparing to a 2001 run. -However, your initial thermodynamic energy and MD trajectory should be -close if you have setup the problem for both codes the same. -

    - diff --git a/doc/doc2/Section_tools.html b/doc/doc2/Section_tools.html deleted file mode 100644 index a68a6138c7..0000000000 --- a/doc/doc2/Section_tools.html +++ /dev/null @@ -1,572 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - LAMMPS -Documentation - LAMMPS Commands - Next -Section -
    - - - - - - -
    - -

    9. Additional tools -

    -

    LAMMPS is designed to be a computational kernel for performing -molecular dynamics computations. Additional pre- and post-processing -steps are often necessary to setup and analyze a simulation. A few -additional tools are provided with the LAMMPS distribution and are -described in this section. -

    -

    Our group has also written and released a separate toolkit called -Pizza.py which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in Python and is available for download from the -Pizza.py WWW site. -

    - - - - -

    Note that many users write their own setup or analysis tools or use -other existing codes and convert their output to a LAMMPS input format -or vice versa. The tools listed here are included in the LAMMPS -distribution as examples of auxiliary tools. Some of them are not -actively supported by Sandia, as they were contributed by LAMMPS -users. If you have problems using them, we can direct you to the -authors. -

    -

    The source code for each of these codes is in the tools sub-directory -of the LAMMPS distribution. There is a Makefile (which you may need -to edit for your platform) which will build several of the tools which -reside in that directory. Some of them are larger packages in their -own sub-directories with their own Makefiles. -

    - -
    - -

    amber2lmp tool -

    -

    The amber2lmp sub-directory contains two Python scripts for converting -files back-and-forth between the AMBER MD code and LAMMPS. See the -README file in amber2lmp for more information. -

    -

    These tools were written by Keir Novik while he was at Queen Mary -University of London. Keir is no longer there and cannot support -these tools which are out-of-date with respect to the current LAMMPS -version (and maybe with respect to AMBER as well). Since we don't use -these tools at Sandia, you'll need to experiment with them and make -necessary modifications yourself. -

    -
    - -

    binary2txt tool -

    -

    The file binary2txt.cpp converts one or more binary LAMMPS dump file -into ASCII text files. The syntax for running the tool is -

    -
    binary2txt file1 file2 ... 
-
    -

    which creates file1.txt, file2.txt, etc. This tool must be compiled -on a platform that can read the binary file created by a LAMMPS run, -since binary files are not compatible across all platforms. -

    -
    - -

    ch2lmp tool -

    -

    The ch2lmp sub-directory contains tools for converting files -back-and-forth between the CHARMM MD code and LAMMPS. -

    -

    They are intended to make it easy to use CHARMM as a builder and as a -post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an -ensemble built in CHARMM into its LAMMPS equivalent. Using -lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files. -

    -

    See the README file in the ch2lmp sub-directory for more information. -

    -

    These tools were created by Pieter in't Veld (pjintve at sandia.gov) -and Paul Crozier (pscrozi at sandia.gov) at Sandia. -

    -
    - -

    chain tool -

    -

    The file chain.f creates a LAMMPS data file containing bead-spring -polymer chains and/or monomer solvent atoms. It uses a text file -containing chain definition parameters as an input. The created -chains and solvent atoms can strongly overlap, so LAMMPS needs to run -the system initially with a "soft" pair potential to un-overlap it. -The syntax for running the tool is -

    -
    chain < def.chain > data.file 
-
    -

    See the def.chain or def.chain.ab files in the tools directory for -examples of definition files. This tool was used to create the -system for the chain benchmark. -

    -
    - -

    colvars tools -

    -

    The colvars directory contains a collection of tools for postprocessing -data produced by the colvars collective variable library. -To compile the tools, edit the makefile for your system and run "make". -

    -

    Please report problems and issues the colvars library and its tools -at: https://github.com/colvars/colvars/issues -

    -

    abf_integrate: -

    -

    MC-based integration of multidimensional free energy gradient -Version 20110511 -

    -
    Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >] 
-
    -

    The LAMMPS interface to the colvars collective variable library, as -well as these tools, were created by Axel Kohlmeyer (akohlmey at -gmail.com) at ICTP, Italy. -

    -
    - -

    createatoms tool -

    -

    The tools/createatoms directory contains a Fortran program called -createAtoms.f which can generate a variety of interesting crystal -structures and geometries and output the resulting list of atom -coordinates in LAMMPS or other formats. -

    -

    See the included Manual.pdf for details. -

    -

    The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. -

    -
    - -

    data2xmovie tool -

    -

    The file data2xmovie.c converts a LAMMPS data file into a snapshot -suitable for visualizing with the xmovie tool, as if it had -been output with a dump command from LAMMPS itself. The syntax for -running the tool is -

    -
    data2xmovie [options] < infile > outfile 
-
    -

    See the top of the data2xmovie.c file for a discussion of the options. -

    -
    - -

    eam database tool -

    -

    The tools/eam_database directory contains a Fortran program that will -generate EAM alloy setfl potential files for any combination of 16 -elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, -Zr. The files can then be used with the pair_style -eam/alloy command. -

    -

    The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, -and is based on his paper: -

    -

    X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, -144113 (2004). -

    -
    - -

    eam generate tool -

    -

    The tools/eam_generate directory contains several one-file C programs -that convert an analytic formula into a tabulated embedded atom -method (EAM) setfl potential file. The potentials they -produce are in the potentials directory, and can be used with the -pair_style eam/alloy command. -

    -

    The source files and potentials were provided by Gerolf Ziegenhain -(gerolf at ziegenhain.com). -

    -
    - -

    eff tool -

    -

    The tools/eff directory contains various scripts for generating -structures and post-processing output for simulations using the -electron force field (eFF). -

    -

    These tools were provided by Andres Jaramillo-Botero at CalTech -(ajaramil at wag.caltech.edu). -

    -
    - -

    emacs tool -

    -

    The tools/emacs directory contains a Lips add-on file for Emacs that -enables a lammps-mode for editing of input scripts when using Emacs, -with various highlighting options setup. -

    -

    These tools were provided by Aidan Thompson at Sandia -(athomps at sandia.gov). -

    -
    - -

    fep tool -

    -

    The tools/fep directory contains Python scripts useful for -post-processing results from performing free-energy perturbation -simulations using the USER-FEP package. -

    -

    The scripts were contributed by Agilio Padua (Universite Blaise -Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr. -

    -

    See README file in the tools/fep directory. -

    -
    - -

    i-pi tool -

    -

    The tools/i-pi directory contains a version of the i-PI package, with -all the LAMMPS-unrelated files removed. It is provided so that it can -be used with the fix ipi command to perform -path-integral molecular dynamics (PIMD). -

    -

    The i-PI package was created and is maintained by Michele Ceriotti, -michele.ceriotti at gmail.com, to interface to a variety of molecular -dynamics codes. -

    -

    See the tools/i-pi/manual.pdf file for an overview of i-PI, and the -fix ipi doc page for further details on running PIMD -calculations with LAMMPS. -

    -
    - -

    ipp tool -

    -

    The tools/ipp directory contains a Perl script ipp which can be used -to facilitate the creation of a complicated file (say, a lammps input -script or tools/createatoms input file) using a template file. -

    -

    ipp was created and is maintained by Reese Jones (Sandia), rjones at -sandia.gov. -

    -

    See two examples in the tools/ipp directory. One of them is for the -tools/createatoms tool's input file. -

    -
    - -

    kate tool -

    -

    The file in the tools/kate directory is an add-on to the Kate editor -in the KDE suite that allow syntax highlighting of LAMMPS input -scripts. See the README.txt file for details. -

    -

    The file was provided by Alessandro Luigi Sellerio -(alessandro.sellerio at ieni.cnr.it). -

    -
    - -

    lmp2arc tool -

    -

    The lmp2arc sub-directory contains a tool for converting LAMMPS output -files to the format for Accelrys' Insight MD code (formerly -MSI/Biosym and its Discover MD code). See the README file for more -information. -

    -

    This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic -(jec at mayo.edu), but still fields questions about the tool. -

    -

    This tool was updated for the current LAMMPS C++ version by Jeff -Greathouse at Sandia (jagreat at sandia.gov). -

    -
    - -

    lmp2cfg tool -

    -

    The lmp2cfg sub-directory contains a tool for converting LAMMPS output -files into a series of *.cfg files which can be read into the -AtomEye visualizer. See -the README file for more information. -

    -

    This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). -

    -
    - -

    lmp2vmd tool -

    -

    The lmp2vmd sub-directory contains a README.txt file that describes -details of scripts and plugin support within the VMD -package for visualizing LAMMPS -dump files. -

    -

    The VMD plugins and other supporting scripts were written by Axel -Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn. -

    -
    - -

    matlab tool -

    -

    The matlab sub-directory contains several MATLAB scripts for -post-processing LAMMPS output. The scripts include readers for log -and dump files, a reader for EAM potential files, and a converter that -reads LAMMPS dump files and produces CFG files that can be visualized -with the AtomEye -visualizer. -

    -

    See the README.pdf file for more information. -

    -

    These scripts were written by Arun Subramaniyan at Purdue Univ -(asubrama at purdue.edu). -

    - - -
    - -

    micelle2d tool -

    -

    The file micelle2d.f creates a LAMMPS data file containing short lipid -chains in a monomer solution. It uses a text file containing lipid -definition parameters as an input. The created molecules and solvent -atoms can strongly overlap, so LAMMPS needs to run the system -initially with a "soft" pair potential to un-overlap it. The syntax -for running the tool is -

    -
    micelle2d < def.micelle2d > data.file 
-
    -

    See the def.micelle2d file in the tools directory for an example of a -definition file. This tool was used to create the system for the -micelle example. -

    -
    - -

    moltemplate tool -

    -

    The moltemplate sub-directory contains a Python-based tool for -building molecular systems based on a text-file description, and -creating LAMMPS data files that encode their molecular topology as -lists of bonds, angles, dihedrals, etc. See the README.TXT file for -more information. -

    -

    This tool was written by Andrew Jewett (jewett.aij at gmail.com), who -supports it. It has its own WWW page at -http://moltemplate.org. -

    -
    - -

    msi2lmp tool -

    -

    The msi2lmp sub-directory contains a tool for creating LAMMPS input -data files from Accelrys' Insight MD code (formerly MSI/Biosym and -its Discover MD code). See the README file for more information. -

    -

    This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic -(jec at mayo.edu), but still fields questions about the tool. -

    -

    This tool may be out-of-date with respect to the current LAMMPS and -Insight versions. Since we don't use it at Sandia, you'll need to -experiment with it yourself. -

    -
    - -

    phonon tool -

    -

    The phonon sub-directory contains a post-processing tool useful for -analyzing the output of the fix phonon command in -the USER-PHONON package. -

    -

    See the README file for instruction on building the tool and what -library it needs. And see the examples/USER/phonon directory -for example problems that can be post-processed with this tool. -

    -

    This tool was written by Ling-Ti Kong at Shanghai Jiao Tong -University. -

    -
    - -

    polymer bonding tool -

    -

    The polybond sub-directory contains a Python-based tool useful for -performing "programmable polymer bonding". The Python file -lmpsdata.py provides a "Lmpsdata" class with various methods which can -be invoked by a user-written Python script to create data files with -complex bonding topologies. -

    -

    See the Manual.pdf for details and example scripts. -

    -

    This tool was written by Zachary Kraus at Georgia Tech. -

    -
    - -

    pymol_asphere tool -

    -

    The pymol_asphere sub-directory contains a tool for converting a -LAMMPS dump file that contains orientation info for ellipsoidal -particles into an input file for the PyMol visualization -package. -

    - - -

    Specifically, the tool triangulates the ellipsoids so they can be -viewed as true ellipsoidal particles within PyMol. See the README and -examples directory within pymol_asphere for more information. -

    -

    This tool was written by Mike Brown at Sandia. -

    -
    - -

    python tool -

    -

    The python sub-directory contains several Python scripts -that perform common LAMMPS post-processing tasks, such as: -

    -
    • extract thermodynamic info from a log file as columns of numbers -
    • plot two columns of thermodynamic info from a log file using GnuPlot -
    • sort the snapshots in a dump file by atom ID -
    • convert multiple NEB dump files into one dump file for viz -
    • convert dump files into XYZ, CFG, or PDB format for viz by other packages -
    -

    These are simple scripts built on Pizza.py modules. See the -README for more info on Pizza.py and how to use these scripts. -

    -
    - -

    reax tool -

    -

    The reax sub-directory contains stand-alond codes that can -post-process the output of the fix reax/bonds -command from a LAMMPS simulation using ReaxFF. See -the README.txt file for more info. -

    -

    These tools were written by Aidan Thompson at Sandia. -

    -
    - -

    restart2data tool -

    -

    IMPORTANT NOTE: This tool is now obsolete and is not included in the -current LAMMPS distribution. This is becaues there is now a -write_data command, which can create a data file -from within an input script. Running LAMMPS with the "-r" -command-line switch as follows: -

    -

    lmp_g++ -r restartfile datafile -

    -

    is the same as running a 2-line input script: -

    -

    read_restart restartfile -write_data datafile -

    -

    which will produce the same data file that the restart2data tool used -to create. The following information is included in case you have an -older version of LAMMPS which still includes the restart2data tool. -

    -

    The file restart2data.cpp converts a binary LAMMPS restart file into -an ASCII data file. The syntax for running the tool is -

    -
    restart2data restart-file data-file (input-file) 
-
    -

    Input-file is optional and if specified will contain LAMMPS input -commands for the masses and force field parameters, instead of putting -those in the data-file. Only a few force field styles currently -support this option. -

    -

    This tool must be compiled on a platform that can read the binary file -created by a LAMMPS run, since binary files are not compatible across -all platforms. -

    -

    Note that a text data file has less precision than a binary restart -file. Hence, continuing a run from a converted data file will -typically not conform as closely to a previous run as will restarting -from a binary restart file. -

    -

    If a "%" appears in the specified restart-file, the tool expects a set -of multiple files to exist. See the restart and -write_restart commands for info on how such sets -of files are written by LAMMPS, and how the files are named. -

    -
    - -

    vim tool -

    -

    The files in the tools/vim directory are add-ons to the VIM editor -that allow easier editing of LAMMPS input scripts. See the README.txt -file for details. -

    -

    These files were provided by Gerolf Ziegenhain (gerolf at -ziegenhain.com) -

    -
    - -

    xmgrace tool -

    -

    The files in the tools/xmgrace directory can be used to plot the -thermodynamic data in LAMMPS log files via the xmgrace plotting -package. There are several tools in the directory that can be used in -post-processing mode. The lammpsplot.cpp file can be compiled and -used to create plots from the current state of a running LAMMPS -simulation. -

    -

    See the README file for details. -

    -

    These files were provided by Vikas Varshney (vv0210 at gmail.com) -

    -
    - -

    xmovie tool -

    -

    The xmovie tool is an X-based visualization package that can read -LAMMPS dump files and animate them. It is in its own sub-directory -with the tools directory. You may need to modify its Makefile so that -it can find the appropriate X libraries to link against. -

    -

    The syntax for running xmovie is -

    -
    xmovie [options] dump.file1 dump.file2 ... 
-
    -

    If you just type "xmovie" you will see a list of options. Note that -by default, LAMMPS dump files are in scaled coordinates, so you -typically need to use the -scale option with xmovie. When xmovie runs -it opens a visualization window and a control window. The control -options are straightforward to use. -

    -

    Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he -spent a summer at Sandia. It displays 2d projections of a 3d domain. -While simple in design, it is an amazingly fast program that can -render large numbers of atoms very quickly. It's a useful tool for -debugging LAMMPS input and output and making sure your simulation is -doing what you think it should. The animations on the Examples page -of the LAMMPS WWW site were created with xmovie. -

    -

    I've lost contact with Mike, so I hope he's comfortable with us -distributing his great tool! -

    - diff --git a/doc/doc2/USER/atc/man_add_molecule.html b/doc/doc2/USER/atc/man_add_molecule.html deleted file mode 100644 index 99270c7276..0000000000 --- a/doc/doc2/USER/atc/man_add_molecule.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - -ATC: fix_modify AtC add_molecule - - - - - - -
    - - -

    fix_modify AtC add_molecule

    -syntax

    -

    fix_modify_AtC add_molecule <small|large> <TAG> <GROUP_NAME>
    -

    -
      -
    • small|large = can be small if molecule size < cutoff radius, must be large otherwise
      -
      • -
    • <TAG> = tag for tracking a species
      -
      • -
    • <GROUP_NAME> = name of group that tracking will be applied to
      -
      • -
    -

    -examples

    -

    group WATERGROUP type 1 2
    - fix_modify AtC add_molecule small water WATERGROUP
    -

    -

    -description

    -

    Associates a tag with all molecules corresponding to a specified group.
    -

    -

    -restrictions

    -

    -related

    -

    -default

    -

    No defaults for this command.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_add_species.html b/doc/doc2/USER/atc/man_add_species.html deleted file mode 100644 index 95192034d9..0000000000 --- a/doc/doc2/USER/atc/man_add_species.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - -ATC: fix_modify AtC add_species - - - - - - -
    - - -

    fix_modify AtC add_species

    -syntax

    -

    fix_modify_AtC add_species <TAG> <group|type> <ID>
    -

    -
      -
    • <TAG> = tag for tracking a species
      -
      • -
    • group|type = LAMMPS defined group or type of atoms
      -
      • -
    • <ID> = name of group or type number
      -
      • -
    -

    -examples

    -

    fix_modify AtC add_species gold type 1
    - group GOLDGROUP type 1
    - fix_modify AtC add_species gold group GOLDGROUP

    -

    -description

    -

    Associates a tag with all atoms of a specified type or within a specified group.
    -

    -

    -restrictions

    -

    -related

    -

    -default

    -

    No defaults for this command.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_atom_element_map.html b/doc/doc2/USER/atc/man_atom_element_map.html deleted file mode 100644 index 3073c0f920..0000000000 --- a/doc/doc2/USER/atc/man_atom_element_map.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC atom_element_map - - - - - - -
    - - -

    fix_modify AtC atom_element_map

    -syntax

    -

    fix_modify AtC atom_element_map <eulerian|lagrangian> <frequency>
    -

    -
      -
    • frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian
      • -
    -

    -examples

    -

    fix_modify atc atom_element_map eulerian 100

    -

    -description

    -

    Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated.

    -

    -restrictions

    -

    Cannot change map type after initialization.

    -

    -related

    -

    -default

    -

    lagrangian

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_atom_weight.html b/doc/doc2/USER/atc/man_atom_weight.html deleted file mode 100644 index 18b0dcae6e..0000000000 --- a/doc/doc2/USER/atc/man_atom_weight.html +++ /dev/null @@ -1,61 +0,0 @@ - - - - -ATC: fix_modify AtC atom_weight - - - - - - -
    - - -

    fix_modify AtC atom_weight

    -syntax

    -

    fix_modify AtC atom_weight <method> <arguments>

    -
      -
    • <method> =
      - value: atoms in specified group assigned constant value given
      - lattice: volume per atom for specified lattice type (e.g. fcc) and parameter
      - element: element volume divided among atoms within element
      - region: volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions.
      - group: volume per atom determined based on the atom count in a group and its volume
      - read_in: list of values for atoms are read-in from specified file
      -
      • -
    -

    -examples

    -

    fix_modify atc atom_weight constant myatoms 11.8
    - fix_modify atc atom_weight lattice
    - fix_modify atc atom_weight read-in atm_wt_file.txt
    -

    -

    -description

    -

    Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations.

    -

    -restrictions

    -

    Use of lattice option requires a lattice type and parameter is already specified.

    -

    -related

    -

    -default

    -

    lattice

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_atomic_charge.html b/doc/doc2/USER/atc/man_atomic_charge.html deleted file mode 100644 index 718f8a433f..0000000000 --- a/doc/doc2/USER/atc/man_atomic_charge.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC atomic_charge - - - - - - -
    - - -

    fix_modify AtC atomic_charge

    -syntax

    -

    fix_modify AtC <include | omit> atomic_charge

    -
      -
    • <include | omit> = switch to activiate/deactiviate inclusion of intrinsic atomic charge in ATC
      • -
    -

    -examples

    -

    fix_modify atc compute include atomic_charge

    -

    -description

    -

    Determines whether AtC tracks the total charge as a finite element field

    -

    -restrictions

    -

    Required for: electrostatics

    -

    -related

    -

    -default

    -

    if the atom charge is defined, default is on, otherwise default is off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_boundary.html b/doc/doc2/USER/atc/man_boundary.html deleted file mode 100644 index 3e877355f1..0000000000 --- a/doc/doc2/USER/atc/man_boundary.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC boundary - - - - - - -
    - - -

    fix_modify AtC boundary

    -syntax

    -

    fix_modify AtC boundary type <atom-type-id>

    -
      -
    • <atom-type-id> = type id for atoms that represent a ficticious boundary internal to the FE mesh
      • -
    -

    -examples

    -

    fix_modify AtC boundary type ghost_atoms

    -

    -description

    -

    Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined.

    -

    -restrictions

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_boundary_dynamics.html b/doc/doc2/USER/atc/man_boundary_dynamics.html deleted file mode 100644 index 87696b8b43..0000000000 --- a/doc/doc2/USER/atc/man_boundary_dynamics.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC boundary_dynamics - - - - - - -
    - - -

    fix_modify AtC boundary_dynamics

    -syntax

    -

    fix_modify AtC boundary_dynamics < on | damped_harmonic | prescribed | coupled | none > [args]
    -

    -

    -description

    -

    Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same.

    -

    -restrictions

    -

    Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two.

    -

    -related

    -

    -default

    -

    prescribed on

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_boundary_faceset.html b/doc/doc2/USER/atc/man_boundary_faceset.html deleted file mode 100644 index 2e96330d6c..0000000000 --- a/doc/doc2/USER/atc/man_boundary_faceset.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC boundary_faceset - - - - - - -
    - - -

    fix_modify AtC boundary_faceset

    -syntax

    -

    fix_modify AtC boundary_faceset <is | add> [args]

    -

    -examples

    -

    fix_modify AtC boundary_faceset is obndy

    -

    -description

    -

    This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist.

    -

    -restrictions

    -

    This is only valid when fe_md_boundary is set to faceset.

    -

    -related

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_boundary_integral.html b/doc/doc2/USER/atc/man_boundary_integral.html deleted file mode 100644 index 3e78f12963..0000000000 --- a/doc/doc2/USER/atc/man_boundary_integral.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC output boundary_integral - - - - - - -
    - - -

    fix_modify AtC output boundary_integral

    -syntax

    -

    fix_modify AtC output boundary_integral [field] faceset [name]

    -
      -
    • field (string) : name of hardy field
      • -
    • name (string) : name of faceset
      • -
    -

    -examples

    -

    fix_modify AtC output boundary_integral stress faceset loop1
    -

    -

    -description

    -

    Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    -

    -related

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_consistent_fe_initialization.html b/doc/doc2/USER/atc/man_consistent_fe_initialization.html deleted file mode 100644 index 2f3bf4a6cf..0000000000 --- a/doc/doc2/USER/atc/man_consistent_fe_initialization.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC consistent_fe_initialization - - - - - - -
    - - -

    fix_modify AtC consistent_fe_initialization

    -syntax

    -

    fix_modify AtC consistent_fe_initialization <on | off>

    -
      -
    • <on|off> = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field
      • -
    -

    -examples

    -

    fix_modify atc consistent_fe_initialization on

    -

    -description

    -

    Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations.

    -

    -restrictions

    -

    Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes.

    -

    -related

    -

    -default

    -

    Default is off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_contour_integral.html b/doc/doc2/USER/atc/man_contour_integral.html deleted file mode 100644 index c321605e88..0000000000 --- a/doc/doc2/USER/atc/man_contour_integral.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC output contour_integral - - - - - - -
    - - -

    fix_modify AtC output contour_integral

    -syntax

    -

    fix_modify AtC output contour_integral [field] faceset [name] <axis [x | y | z ]>

    -
      -
    • field (string) : name of hardy field
      • -
    • name (string) : name of faceset
      • -
    • axis (string) : x or y or z
      • -
    -

    -examples

    -

    fix_modify AtC output contour_integral stress faceset loop1
    -

    -

    -description

    -

    Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    -

    -related

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_control.html b/doc/doc2/USER/atc/man_control.html deleted file mode 100644 index af0236f30e..0000000000 --- a/doc/doc2/USER/atc/man_control.html +++ /dev/null @@ -1,72 +0,0 @@ - - - - -ATC: fix_modify AtC control - - - - - - -
    - - -

    fix_modify AtC control

    -syntax

    -

    fix_modify AtC control <physics_type> <solution_parameter>

    -


    -

    -
      -
    • physics_type (string) = thermal | momentum
      -
      • -
    • solution_parameter (string) = max_iterations | tolerance
      -
      • -
    -

    fix_modify AtC transfer <physics_type> control max_iterations <max_iterations>
    -

    -
      -
    • max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers
      -
      • -
    -

    fix_modify AtC transfer <physics_type> control tolerance <tolerance>
    -

    -
      -
    • tolerance (float) = relative tolerance to which matrix equations will be solved
      -
      • -
    -

    -examples

    -

    fix_modify AtC control thermal max_iterations 10
    - fix_modify AtC control momentum tolerance 1.e-5
    -

    -

    -description

    -

    Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance.

    -

    -restrictions

    -

    only for be used with specific controllers : thermal, momentum
    - They are ignored if a lumped solution is requested

    -

    -related

    -

    -default

    -

    max_iterations is the number of rows in the matrix
    - tolerance is 1.e-10

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_control_momentum.html b/doc/doc2/USER/atc/man_control_momentum.html deleted file mode 100644 index 805c12567a..0000000000 --- a/doc/doc2/USER/atc/man_control_momentum.html +++ /dev/null @@ -1,68 +0,0 @@ - - - - -ATC: fix_modify AtC control momentum - - - - - - -
    - - -

    fix_modify AtC control momentum

    -syntax

    -

    fix_modify AtC control momentum none
    -

    -

    fix_modify AtC control momentum rescale <frequency>
    -

    -
      -
    • frequency (int) = time step frequency for applying displacement and velocity rescaling
      -
      • -
    -

    fix_modify AtC control momentum glc_displacement
    -

    -

    fix_modify AtC control momentum glc_velocity
    -

    -

    fix_modify AtC control momentum hoover
    -

    -

    fix_modify AtC control momentum flux [faceset face_set_id, interpolate]

    -
      -
    • face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation
      -
      • -
    -

    -examples

    -

    fix_modify AtC control momentum glc_velocity
    - fix_modify AtC control momentum flux faceset bndy_faces
    -

    -

    -description

    -

    -restrictions

    -

    only to be used with specific transfers : elastic
    - rescale not valid with time filtering activated

    -

    -related

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_control_thermal.html b/doc/doc2/USER/atc/man_control_thermal.html deleted file mode 100644 index 301297f306..0000000000 --- a/doc/doc2/USER/atc/man_control_thermal.html +++ /dev/null @@ -1,76 +0,0 @@ - - - - -ATC: fix_modify AtC control thermal - - - - - - -
    - - -

    fix_modify AtC control thermal

    -syntax

    -

    fix_modify AtC control thermal <control_type> <optional_args>

    -
      -
    • control_type (string) = none | rescale | hoover | flux
      -
      • -
    -

    fix_modify AtC control thermal rescale <frequency>
    -

    -
      -
    • frequency (int) = time step frequency for applying velocity rescaling
      -
      • -
    -

    fix_modify AtC control thermal hoover
    -

    -

    fix_modify AtC control thermal flux <boundary_integration_type(optional)> <face_set_id(optional)>
    -

    -
      -
    • boundary_integration_type (string) = faceset | interpolate
      -
      • -
    • face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate
      -
      • -
    -

    -examples

    -

    fix_modify AtC control thermal none
    - fix_modify AtC control thermal rescale 10
    - fix_modify AtC control thermal hoover
    - fix_modify AtC control thermal flux
    - fix_modify AtC control thermal flux faceset bndy_faces
    -

    -

    -description

    -

    Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms.

    -

    -restrictions

    -

    only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux)
    - rescale not valid with time filtering activated

    -

    -related

    -

    -default

    -

    none
    - rescale frequency is 1
    - flux boundary_integration_type is interpolate

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/doc2/USER/atc/man_control_thermal_correction_max_iterations.html deleted file mode 100644 index 8a511019f9..0000000000 --- a/doc/doc2/USER/atc/man_control_thermal_correction_max_iterations.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC control thermal correction_max_iterations - - - - - - -
    - - -

    fix_modify AtC control thermal correction_max_iterations

    -syntax

    -

    fix_modify AtC control thermal correction_max_iterations <max_iterations>

    -
      -
    • max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers
      -
      • -
    -

    -examples

    -

    fix_modify AtC control thermal correction_max_iterations 10
    -

    -

    -description

    -

    Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver.

    -

    -restrictions

    -

    only for use with thermal physics using the fractional step method.

    -

    -related

    -

    -default

    -

    correction_max_iterations is 20

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_decomposition.html b/doc/doc2/USER/atc/man_decomposition.html deleted file mode 100644 index 15725073d3..0000000000 --- a/doc/doc2/USER/atc/man_decomposition.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - -ATC: fix_modify AtC decomposition - - - - - - -
    - - -

    fix_modify AtC decomposition

    -syntax

    -

    fix_modify AtC decomposition <type>

    -
      -
    • <type> =
      - replicated_memory: nodal information replicated on each processor
      - distributed_memory: only owned nodal information on processor
      -
      • -
    -

    -examples

    -

    fix_modify atc decomposition distributed_memory
    -

    -

    -description

    -

    Command for assigning the distribution of work and memory for parallel runs.

    -

    -restrictions

    -

    replicated_memory is appropriate for simulations were the number of nodes << number of atoms

    -

    -related

    -

    -default

    -

    replicated_memory

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_electron_integration.html b/doc/doc2/USER/atc/man_electron_integration.html deleted file mode 100644 index b14c14d86d..0000000000 --- a/doc/doc2/USER/atc/man_electron_integration.html +++ /dev/null @@ -1,56 +0,0 @@ - - - - -ATC: fix_modify AtC extrinsic electron_integration - - - - - - -
    - - -

    fix_modify AtC extrinsic electron_integration

    -syntax

    -

    fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)>
    -

    -
      -
    • integration_type (string) = explicit | implicit | steady
      -
      • -
    • num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration
      • -
    -

    -examples

    -

    fix_modify AtC extrinsic electron_integration implicit
    - fix_modify AtC extrinsic electron_integration explicit 100
    -

    -

    -description

    -

    Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.

    -

    -restrictions

    -

    For use only with two_temperature type of AtC fix ( see fix atc command )
    -

    -

    -default

    -

    implicit
    - subcycle_steps = 1

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_equilibrium_start.html b/doc/doc2/USER/atc/man_equilibrium_start.html deleted file mode 100644 index 3723cf98bf..0000000000 --- a/doc/doc2/USER/atc/man_equilibrium_start.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC equilibrium_start - - - - - - -
    - - -

    fix_modify AtC equilibrium_start

    -syntax

    -

    fix_modify AtC equilibrium_start <on|off>

    -

    -examples

    -

    fix_modify atc equilibrium_start on
    -

    -

    -description

    -

    Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.

    -

    -restrictions

    -

    only needed before filtering is begun

    -

    -related

    -

    see fix_modify AtC filter

    -

    -default

    -

    on

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_extrinsic_exchange.html b/doc/doc2/USER/atc/man_extrinsic_exchange.html deleted file mode 100644 index 8f6533ad64..0000000000 --- a/doc/doc2/USER/atc/man_extrinsic_exchange.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC extrinsic exchange - - - - - - -
    - - -

    fix_modify AtC extrinsic exchange

    -syntax

    -

    fix_modify AtC extrinsic exchange <on|off>

    -

    -examples

    -

    fix_modify AtC extrinsic exchange on
    -

    -

    -description

    -

    Switches energy exchange between the MD system and electron system on and off

    -

    -restrictions

    -

    Only valid for use with two_temperature type of AtC fix.

    -

    -related

    -

    see fix atc command

    -

    -default

    -

    on

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_fe_md_boundary.html b/doc/doc2/USER/atc/man_fe_md_boundary.html deleted file mode 100644 index 06bca2b337..0000000000 --- a/doc/doc2/USER/atc/man_fe_md_boundary.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC fe_md_boundary - - - - - - -
    - - -

    fix_modify AtC fe_md_boundary

    -syntax

    -

    fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args]

    -

    -examples

    -

    fix_modify atc fe_md_boundary interpolate
    -

    -

    -description

    -

    Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed.

    -

    -restrictions

    -

    If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.

    -

    -related

    -

    see for how to specify the faceset name.

    -

    -default

    -

    Interpolate.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_fem_mesh.html b/doc/doc2/USER/atc/man_fem_mesh.html deleted file mode 100644 index 2abd84d6ce..0000000000 --- a/doc/doc2/USER/atc/man_fem_mesh.html +++ /dev/null @@ -1,25 +0,0 @@ - - -ATC: fix_modify AtC fem create mesh - - - -

    fix_modify AtC fem create mesh

    -syntax

    -fix_modify AtC fem create mesh <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
      -
    • nx ny nz = number of elements in x, y, z
    • region-id = id of region that is to be meshed
    • f p p = perioidicity flags for x, y, z
    -

    -examples

    - fix_modify AtC fem create mesh 10 1 1 feRegion p p p

    -description

    -Creates a uniform mesh in a rectangular region

    -restrictions

    -creates only uniform rectangular grids in a rectangular region

    -related

    -

    -default

    -none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  - -doxygen 1.3.9.1
    - - diff --git a/doc/doc2/USER/atc/man_filter_scale.html b/doc/doc2/USER/atc/man_filter_scale.html deleted file mode 100644 index 975f87e949..0000000000 --- a/doc/doc2/USER/atc/man_filter_scale.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - -ATC: fix_modify AtC filter scale - - - - - - -
    - - -

    fix_modify AtC filter scale

    -syntax

    -

    fix_modify AtC filter scale <scale>
    -

    -
      -
    • scale (real) = characteristic time scale of the filter
      -
      • -
    -

    -examples

    -

    fix_modify AtC filter scale 10.0
    -

    -

    -description

    -

    Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics

    -

    -restrictions

    -

    only for be used with specific transfers: thermal, two_temperature

    -

    -related

    -

    fix_modify AtC filter fix_modify AtC filter type

    -

    -default

    -

    0.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_filter_type.html b/doc/doc2/USER/atc/man_filter_type.html deleted file mode 100644 index 8d9dbd3d12..0000000000 --- a/doc/doc2/USER/atc/man_filter_type.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC filter type - - - - - - -
    - - -

    fix_modify AtC filter type

    -syntax

    -

    fix_modify AtC filter type <exponential | step | no_filter>
    -

    -

    -examples

    -

    fix_modify AtC filter type exponential
    -

    -

    -description

    -

    Specifies the type of time filter used.

    -

    -restrictions

    -

    only for be used with specific transfers: thermal, two_temperature

    -

    -related

    -

    fix_modify AtC filter fix_modify AtC filter scale

    -

    -default

    -

    No default.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_fix_atc.html b/doc/doc2/USER/atc/man_fix_atc.html deleted file mode 100644 index e710c28ed2..0000000000 --- a/doc/doc2/USER/atc/man_fix_atc.html +++ /dev/null @@ -1,254 +0,0 @@ - - - - -ATC: fix atc command - - - - - - -
    - - -

    fix atc command

    -syntax

    -

    fix <fixID> <group> atc <type> <parameter_file>

    -
      -
    • fixID = name of fix
      • -
    • group = name of group fix is to be applied
      • -
    • type
      - = thermal : thermal coupling with fields: temperature
      - = two_temperature : electron-phonon coupling with field: temperature and electron_temperature
      - = hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
      - = field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
      -
      • -
    • parameter_file = name of the file with material parameters.
      - note: Neither hardy nor field requires a parameter file
      • -
    -

    -examples

    -

    fix AtC internal atc thermal Ar_thermal.dat
    - fix AtC internal atc two_temperature Ar_ttm.mat
    - fix AtC internal atc hardy
    - fix AtC internal atc field
    -

    -

    -description

    -

    This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.

    -

    The following coupling example is typical, but non-exhaustive:
    -

    -

    # ... commands to create and initialize the MD system
    -

    -

    # initial fix to designate coupling type and group to apply it to
    - # tag group physics material_file
    - fix AtC internal atc thermal Ar_thermal.mat
    -
    - # create a uniform 12 x 2 x 2 mesh that covers region contain the group
    - # nx ny nz region periodicity
    - fix_modify AtC mesh create 12 2 2 mdRegion f p p
    -
    - # specify the control method for the type of coupling
    - # physics control_type
    - fix_modify AtC thermal control flux
    -
    - # specify the initial values for the empirical field "temperature"
    - # field node_group value
    - fix_modify AtC initial temperature all 30.
    -
    - # create an output stream for nodal fields
    - # filename output_frequency
    - fix_modify AtC output atc_fe_output 100
    -
    -

    -

    run 1000
    -

    -

    likewise for this post-processing example:
    -

    -

    # ... commands to create and initialize the MD system
    -

    -

    # initial fix to designate post-processing and the group to apply it to
    - # no material file is allowed nor required
    - fix AtC internal atc hardy
    -
    - # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
    - fix AtC kernel quartic_sphere 10.0
    -
    - # create a uniform 1 x 1 x 1 mesh that covers region contain the group
    - # with periodicity this effectively creats a system average
    - fix_modify AtC mesh create 1 1 1 box p p p
    -
    - # change from default lagrangian map to eulerian
    - # refreshed every 100 steps
    - fix_modify AtC atom_element_map eulerian 100
    -
    - # start with no field defined
    - # add mass density, potential energy density, stress and temperature
    - fix_modify AtC fields add density energy stress temperature
    -
    - # create an output stream for nodal fields
    - # filename output_frequency
    - fix_modify AtC output nvtFE 100 text
    -

    -

    run 1000
    -

    -

    the mesh's linear interpolation functions can be used as the localization function
    - by using the field option:
    -

    -

    fix AtC internal atc field
    -
    - fix_modify AtC mesh create 1 1 1 box p p p
    -
    - ...
    -
    -

    -

    Note coupling and post-processing can be combined in the same simulations using separate fixes.
    - For detailed exposition of the theory and algorithms please see:
    -

    -
      -
    • Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, An atomistic-to-continuum coupling method for heat transfer in solids. Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
      -
      • -
    • Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, Calculation of stress in atomistic simulation. Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
      -
      • -
    • Zimmerman, JA; Jones, RE; Templeton, JA, A material frame approach for evaluating continuum variables in atomistic simulations. Journal of Computational Physics (2010), 229:2364.
      -
      • -
    • Templeton, JA; Jones, RE; Wagner, GJ, Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
      -
      • -
    • Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, Electron transport enhanced molecular dynamics for metals and semi-metals. International Journal for Numerical Methods in Engineering (2010), 83:940.
      -
      • -
    • Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. Journal of Chemical Theory and Computation (2011), 7:1736.
      -
      • -
    • Mandadapu, KK; Templeton, JA; Lee, JW, Polarization as a field variable from molecular dynamics simulations. Journal of Chemical Physics (2013), 139:054115.
      -
      • -
    -

    Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes The finite element method , Dover 2003, for the basics of FE simulation.

    -

    -restrictions

    -

    Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.

    -

    Currently,

    -
      -
    • the coupling is restricted to thermal physics
      • -
    • the FE computations are done in serial on each processor.
      • -
    -

    -related

    -

    fix_modify commands for setup:
    -

    - -

    fix_modify commands for boundary and initial conditions:
    -

    - -

    fix_modify commands for control and filtering:
    -

    - -

    fix_modify commands for output:
    -

    - -

    fix_modify commands for post-processing:
    -

    - -

    miscellaneous fix_modify commands:
    -

    - -

    Note: a set of example input files with the attendant material files are included with this package

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_fix_flux.html b/doc/doc2/USER/atc/man_fix_flux.html deleted file mode 100644 index d8369a8785..0000000000 --- a/doc/doc2/USER/atc/man_fix_flux.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC fix_flux - - - - - - -
    - - -

    fix_modify AtC fix_flux

    -syntax

    -

    fix_modify AtC fix_flux <field> <face_set> <value | function>

    -
      -
    • <field> = field name valid for type of physics, temperature | electron_temperature
      • -
    • <face_set> = name of set of element faces
      • -
    -

    -examples

    -

    fix_modify atc fix_flux temperature faceSet 10.0
    -

    -

    -description

    -

    Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales.

    -

    -restrictions

    -

    Only normal fluxes (Neumann data) can be prescribed.

    -

    -related

    -

    see fix_modify AtC unfix_flux

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_fix_nodes.html b/doc/doc2/USER/atc/man_fix_nodes.html deleted file mode 100644 index cf5c93590a..0000000000 --- a/doc/doc2/USER/atc/man_fix_nodes.html +++ /dev/null @@ -1,56 +0,0 @@ - - - - -ATC: fix_modify AtC fix - - - - - - -
    - - -

    fix_modify AtC fix

    -syntax

    -

    fix_modify AtC fix <field> <nodeset> <constant | function>

    -
      -
    • <field> = field name valid for type of physics
      • -
    • <nodeset> = name of set of nodes to apply boundary condition
      • -
    • <constant | function> = value or name of function followed by its parameters
      • -
    -

    -examples

    -

    fix_modify AtC fix temperature groupNAME 10.
    - fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0
    -

    -

    -description

    -

    Creates a constraint on the values of the specified field at specified nodes.

    -

    -restrictions

    -

    keyword 'all' reserved in nodeset name

    -

    -related

    -

    see fix_modify AtC unfix

    -

    -default

    -

    none

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_hardy_computes.html b/doc/doc2/USER/atc/man_hardy_computes.html deleted file mode 100644 index c16550742b..0000000000 --- a/doc/doc2/USER/atc/man_hardy_computes.html +++ /dev/null @@ -1,67 +0,0 @@ - - - - -ATC: fix_modify AtC computes - - - - - - -
    - - -

    fix_modify AtC computes

    -syntax

    -

    fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number>
    -

    -
      -
    • add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity
      -
      • -
    • per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS
      -
      • -
    • volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions
      -
      • -
    -

    -examples

    -

    compute virial all stress/atom
    - fix_modify AtC computes add virial volume
    - fix_modify AtC computes delete virial
    -
    - compute centrosymmetry all centro/atom
    - fix_modify AtC computes add centrosymmetry number
    -

    -

    -description

    -

    Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS
    -

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix ( see fix atc command )
    - Per-atom compute must be specified before corresponding continuum field can be requested
    -

    -

    -related

    -

    See manual page for compute

    -

    -default

    -

    No defaults exist for this command

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_hardy_fields.html b/doc/doc2/USER/atc/man_hardy_fields.html deleted file mode 100644 index 1f55fd5e37..0000000000 --- a/doc/doc2/USER/atc/man_hardy_fields.html +++ /dev/null @@ -1,83 +0,0 @@ - - - - -ATC: fix_modify AtC fields - - - - - - -
    - - -

    fix_modify AtC fields

    -syntax

    -

    fix_modify AtC fields <all | none>
    - fix_modify AtC fields <add | delete> <list_of_fields>
    -

    -
      -
    • all | none (keyword) = output all or no fields
      -
      • -
    • add | delete (keyword) = add or delete the listed output fields
      -
      • -
    • fields (keyword) =
      - density : mass per unit volume
      - displacement : displacement vector
      - momentum : momentum per unit volume
      - velocity : defined by momentum divided by density
      - projected_velocity : simple kernel estimation of atomic velocities
      - temperature : temperature derived from the relative atomic kinetic energy (as done by )
      - kinetic_temperature : temperature derived from the full kinetic energy
      - number_density : simple kernel estimation of number of atoms per unit volume
      - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
      - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
      - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
      - potential_energy : potential energy per unit volume
      - kinetic_energy : kinetic energy per unit volume
      - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume
      - internal_energy : total internal energy (potential + thermal) per unit volume
      - energy : total energy (potential + kinetic) per unit volume
      - number_density : number of atoms per unit volume
      - eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby [References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
      - vacancy_concentration: volume fraction of vacancy content
      - type_concentration: volume fraction of a specific atom type
      -
      • -
    -

    -examples

    -

    fix_modify AtC fields add velocity temperature

    -

    -description

    -

    Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.
    - fix_modify AtC fields none
    - followed by
    - fix_modify AtC fields add velocity temperature
    - will only output the velocity and temperature fields.

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix, see fix atc command. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber.

    -

    -related

    -

    See fix_modify AtC gradients , fix_modify AtC rates and fix_modify AtC computes

    -

    -default

    -

    By default, no fields are output

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_hardy_gradients.html b/doc/doc2/USER/atc/man_hardy_gradients.html deleted file mode 100644 index 708fecbca1..0000000000 --- a/doc/doc2/USER/atc/man_hardy_gradients.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC gradients - - - - - - -
    - - -

    fix_modify AtC gradients

    -syntax

    -

    fix_modify AtC gradients <add | delete> <list_of_fields>
    -

    -
      -
    • add | delete (keyword) = add or delete the calculation of gradients for the listed output fields
      -
      • -
    • fields (keyword) =
      - gradients can be calculated for all fields listed in fix_modify AtC fields
      • -
    -

    -examples

    -

    fix_modify AtC gradients add temperature velocity stress
    - fix_modify AtC gradients delete velocity
    -

    -

    -description

    -

    Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see fix_modify AtC atom_element_map )

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    -

    -related

    -

    -default

    -

    No gradients are calculated by default

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_hardy_kernel.html b/doc/doc2/USER/atc/man_hardy_kernel.html deleted file mode 100644 index 3d81b367dd..0000000000 --- a/doc/doc2/USER/atc/man_hardy_kernel.html +++ /dev/null @@ -1,65 +0,0 @@ - - - - -ATC: fix_modify AtC kernel - - - - - - -
    - - -

    fix_modify AtC kernel

    -syntax

    -

    fix_modify AtC kernel <type> <parameters>

    -
      -
    • type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
      -
      • -
    • parameters :
      - step = radius (double)
      - cell = hx, hy, hz (double) or h (double)
      - cubic_bar = half-width (double)
      - cubic_cylinder = radius (double)
      - cubic_sphere = radius (double)
      - quartic_bar = half-width (double)
      - quartic_cylinder = radius (double)
      - quartic_sphere = radius (double)
      -
      • -
    -

    -examples

    -

    fix_modify AtC kernel cell 1.0 1.0 1.0
    - fix_modify AtC kernel quartic_sphere 10.0

    -

    -description

    -

    -restrictions

    -

    Must be used with the hardy AtC fix
    - For bar kernel types, half-width oriented along x-direction
    - For cylinder kernel types, cylindrical axis is assumed to be in z-direction
    - ( see fix atc command )

    -

    -related

    -

    -default

    -

    No default

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_hardy_on_the_fly.html b/doc/doc2/USER/atc/man_hardy_on_the_fly.html deleted file mode 100644 index d140cf6840..0000000000 --- a/doc/doc2/USER/atc/man_hardy_on_the_fly.html +++ /dev/null @@ -1,60 +0,0 @@ - - - - -ATC: fix_modify AtC on_the_fly - - - - - - -
    - - -

    fix_modify AtC on_the_fly

    -syntax

    -

    fix_modify AtC on_the_fly <bond | kernel> <optional on | off>
    - - bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements
    -

    -
      -
    • on | off (keyword) = activate or discontinue on-the-fly mode
      -
      • -
    -

    -examples

    -

    fix_modify AtC on_the_fly bond on
    - fix_modify AtC on_the_fly kernel
    - fix_modify AtC on_the_fly kernel off
    -

    -

    -description

    -

    Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use.
    - on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag.
    -

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    -

    -related

    -

    -default

    -

    By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated.
    -

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_hardy_rates.html b/doc/doc2/USER/atc/man_hardy_rates.html deleted file mode 100644 index ab0315cb65..0000000000 --- a/doc/doc2/USER/atc/man_hardy_rates.html +++ /dev/null @@ -1,58 +0,0 @@ - - - - -ATC: fix_modify AtC rates - - - - - - -
    - - -

    fix_modify AtC rates

    -syntax

    -

    fix_modify AtC rates <add | delete> <list_of_fields>
    -

    -
      -
    • add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields
      -
      • -
    • fields (keyword) =
      - rates can be calculated for all fields listed in fix_modify AtC fields
      • -
    -

    -examples

    -

    fix_modify AtC rates add temperature velocity stress
    - fix_modify AtC rates delete stress
    -

    -

    -description

    -

    Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see fix_modify AtC atom_element_map ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives.
    -

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    -

    -related

    -

    -default

    -

    No rates are calculated by default

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_initial.html b/doc/doc2/USER/atc/man_initial.html deleted file mode 100644 index c0a0be3852..0000000000 --- a/doc/doc2/USER/atc/man_initial.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC initial - - - - - - -
    - - -

    fix_modify AtC initial

    -syntax

    -

    fix_modify AtC initial <field> <nodeset> <constant | function>

    -
      -
    • <field> = field name valid for type of physics, temperature | electron_temperature
      • -
    • <nodeset> = name of set of nodes to apply initial condition
      • -
    • <constant | function> = value or name of function followed by its parameters
      • -
    -

    -examples

    -

    fix_modify atc initial temperature groupNAME 10.

    -

    -description

    -

    Sets the initial values for the specified field at the specified nodes.

    -

    -restrictions

    -

    keyword 'all' reserved in nodeset name

    -

    -default

    -

    none

    -
    -
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    - - diff --git a/doc/doc2/USER/atc/man_internal_atom_integrate.html b/doc/doc2/USER/atc/man_internal_atom_integrate.html deleted file mode 100644 index b15bf71aad..0000000000 --- a/doc/doc2/USER/atc/man_internal_atom_integrate.html +++ /dev/null @@ -1,40 +0,0 @@ - - - - -ATC: fix_modify AtC internal_atom_integrate - - - - - - -
    - - -

    fix_modify AtC internal_atom_integrate

    -syntax

    -

    fix_modify AtC internal_atom_integrate <on | off> fix_modify AtC internal_atom_integrate on

    -

    -description

    -

    Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms.

    -

    -default

    -

    on for coupling methods, off for post-processors off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_internal_element_set.html b/doc/doc2/USER/atc/man_internal_element_set.html deleted file mode 100644 index 31bee57860..0000000000 --- a/doc/doc2/USER/atc/man_internal_element_set.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC internal_element_set - - - - - - -
    - - -

    fix_modify AtC internal_element_set

    -syntax

    -

    fix_modify AtC internal_element_set <element-set-name>

    -
      -
    • <element-set-name> = name of element set defining internal region, or off
      • -
    -

    -examples

    -

    fix_modify AtC internal_element_set myElementSet fix_modify AtC internal_element_set off

    -

    -description

    -

    Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise.

    -

    -restrictions

    -

    If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency

    -

    -related

    -

    see atom_element_map_type and boundary

    -

    -default

    -

    off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_internal_quadrature.html b/doc/doc2/USER/atc/man_internal_quadrature.html deleted file mode 100644 index 172187c298..0000000000 --- a/doc/doc2/USER/atc/man_internal_quadrature.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC internal_quadrature - - - - - - -
    - - -

    fix_modify AtC internal_quadrature

    -syntax

    -

    fix_modify atc internal_quadrature <on | off> [region]

    -

    -examples

    -

    fix_modify atc internal_quadrature off

    -

    -description

    -

    Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data.

    -

    -optional

    -

    Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off.

    -

    -restrictions

    -

    -related

    -

    -default

    -

    on

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_kernel_function.html b/doc/doc2/USER/atc/man_kernel_function.html deleted file mode 100644 index 08ec827dec..0000000000 --- a/doc/doc2/USER/atc/man_kernel_function.html +++ /dev/null @@ -1,64 +0,0 @@ - - - - -ATC: fix_modify AtC kernel - - - - - - -
    - - -

    fix_modify AtC kernel

    -syntax

    -

    fix_modify AtC kernel <type> <parameters>

    -
      -
    • type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
      -
      • -
    • parameters :
      - step = radius (double)
      - cell = hx, hy, hz (double) or h (double)
      - cubic_bar = half-width (double)
      - cubic_cylinder = radius (double)
      - cubic_sphere = radius (double)
      - quartic_bar = half-width (double)
      - quartic_cylinder = radius (double)
      - quartic_sphere = radius (double)
      -
      • -
    -

    -examples

    -

    fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0

    -

    -description

    -

    -restrictions

    -

    Must be used with the hardy AtC fix
    - For bar kernel types, half-width oriented along x-direction
    - For cylinder kernel types, cylindrical axis is assumed to be in z-direction
    - ( see fix atc command )

    -

    -related

    -

    -default

    -

    No default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_localized_lambda.html b/doc/doc2/USER/atc/man_localized_lambda.html deleted file mode 100644 index 5dadb9d730..0000000000 --- a/doc/doc2/USER/atc/man_localized_lambda.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC control localized_lambda - - - - - - -
    - - -

    fix_modify AtC control localized_lambda

    -syntax

    -

    fix_modify AtC control localized_lambda <on|off>

    -

    -examples

    -

    fix_modify atc control localized_lambda on
    -

    -

    -description

    -

    Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation.

    -

    -restrictions

    -

    -related

    -

    -default

    -

    Default is off.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_lumped_lambda_solve.html b/doc/doc2/USER/atc/man_lumped_lambda_solve.html deleted file mode 100644 index bb3f8cfde8..0000000000 --- a/doc/doc2/USER/atc/man_lumped_lambda_solve.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC control lumped_lambda_solve - - - - - - -
    - - -

    fix_modify AtC control lumped_lambda_solve

    -syntax

    -

    fix_modify AtC control lumped_lambda_solve <on|off>

    -

    -examples

    -

    fix_modify atc control lumped_lambda_solve on
    -

    -

    -description

    -

    Command to use or not use lumped matrix for lambda solve

    -

    -restrictions

    -

    -related

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mask_direction.html b/doc/doc2/USER/atc/man_mask_direction.html deleted file mode 100644 index 01ca9d192b..0000000000 --- a/doc/doc2/USER/atc/man_mask_direction.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC control mask_direction - - - - - - -
    - - -

    fix_modify AtC control mask_direction

    -syntax

    -

    fix_modify AtC control mask_direction <direction> <on|off>

    -

    -examples

    -

    fix_modify atc control mask_direction 0 on
    -

    -

    -description

    -

    Command to mask out certain dimensions from the atomic regulator

    -

    -restrictions

    -

    -related

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mass_matrix.html b/doc/doc2/USER/atc/man_mass_matrix.html deleted file mode 100644 index 5f543fc20c..0000000000 --- a/doc/doc2/USER/atc/man_mass_matrix.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC mass_matrix - - - - - - -
    - - -

    fix_modify AtC mass_matrix

    -syntax

    -

    fix_modify AtC mass_matrix <fe | md_fe>

    -
      -
    • <fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region
      • -
    -

    -examples

    -

    fix_modify atc mass_matrix fe

    -

    -description

    -

    Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency.

    -

    -restrictions

    -

    Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate

    -

    -related

    -

    -default

    -

    Default is off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_material.html b/doc/doc2/USER/atc/man_material.html deleted file mode 100644 index 9867e90f77..0000000000 --- a/doc/doc2/USER/atc/man_material.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC material - - - - - - -
    - - -

    fix_modify AtC material

    -syntax

    -

    fix_modify AtC material [elementset_name] [material_id]
    -

    -

    -examples

    -

    fix_modify AtC material gap_region 2

    -

    -description

    -

    Sets the material model in elementset_name to be of type material_id.

    -

    -restrictions

    -

    The element set must already be created and the material must be specified in the material file given the the atc fix on construction

    -

    -related

    -

    -default

    -

    All elements default to the first material in the material file.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_add_to_nodeset.html b/doc/doc2/USER/atc/man_mesh_add_to_nodeset.html deleted file mode 100644 index cf5ad52f60..0000000000 --- a/doc/doc2/USER/atc/man_mesh_add_to_nodeset.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC mesh add_to_nodeset - - - - - - -
    - - -

    fix_modify AtC mesh add_to_nodeset

    -syntax

    -

    fix_modify AtC mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

    -
      -
    • <id> = id of FE nodeset to be added to
      • -
    • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added
      • -
    -

    -examples

    -

    fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12

    -

    -description

    -

    Command to add nodes to an already existing FE nodeset.

    -

    -restrictions

    -

    -related

    -

    -default

    -

    Coordinates are assumed to be in lattice units.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_create.html b/doc/doc2/USER/atc/man_mesh_create.html deleted file mode 100644 index efaf7f4307..0000000000 --- a/doc/doc2/USER/atc/man_mesh_create.html +++ /dev/null @@ -1,56 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create - - - - - - -
    - - -

    fix_modify AtC mesh create

    -syntax

    -

    fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
    -

    -
      -
    • nx ny nz = number of elements in x, y, z
      • -
    • region-id = id of region that is to be meshed
      • -
    • f p p = periodicity flags for x, y, z
      • -
    -

    -examples

    -

    fix_modify AtC mesh create 10 1 1 feRegion p p p
    -

    -

    -description

    -

    Creates a uniform mesh in a rectangular region

    -

    -restrictions

    -

    Creates only uniform rectangular grids in a rectangular region

    -

    -related

    -

    fix_modify AtC mesh quadrature

    -

    -default

    -

    When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_create_elementset.html b/doc/doc2/USER/atc/man_mesh_create_elementset.html deleted file mode 100644 index 51bdae4faa..0000000000 --- a/doc/doc2/USER/atc/man_mesh_create_elementset.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_elementset - - - - - - -
    - - -

    fix_modify AtC mesh create_elementset

    -syntax

    -

    fix_modify AtC create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

    -
      -
    • <id> = id to assign to the collection of FE element
      • -
    • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements
      • -
    -

    -examples

    -

    fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100

    -

    -description

    -

    Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations.

    -

    -restrictions

    -

    Only viable for rectangular grids.

    -

    -related

    -

    -default

    -

    Coordinates are assumed to be in lattice units.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_create_faceset_box.html b/doc/doc2/USER/atc/man_mesh_create_faceset_box.html deleted file mode 100644 index 163a6b442c..0000000000 --- a/doc/doc2/USER/atc/man_mesh_create_faceset_box.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_faceset box - - - - - - -
    - - -

    fix_modify AtC mesh create_faceset box

    -syntax

    -

    fix_modify AtC mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]

    -
      -
    • <id> = id to assign to the collection of FE faces
      • -
    • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that is coincident with the desired FE faces
      • -
    • <in|out> = "in" gives inner faces to the box, "out" gives the outer faces to the box
      • -
    • units = option to specify real as opposed to lattice units
      • -
    -

    -examples

    -

    fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out

    -

    -description

    -

    Command to assign an id to a set of FE faces.

    -

    -restrictions

    -

    Only viable for rectangular grids.

    -

    -related

    -

    -default

    -

    The default options are units = lattice and the use of outer faces

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_create_faceset_plane.html b/doc/doc2/USER/atc/man_mesh_create_faceset_plane.html deleted file mode 100644 index 3ca1108d1a..0000000000 --- a/doc/doc2/USER/atc/man_mesh_create_faceset_plane.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_faceset plane - - - - - - -
    - - -

    fix_modify AtC mesh create_faceset plane

    -syntax

    -

    fix_modify AtC mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]

    -
      -
    • <id> = id to assign to the collection of FE faces
      • -
    • <x|y|z> = coordinate directions that define plane on which faceset lies
      • -
    • <val1>,<lval2>,<uval2> = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]
      • -
    • units = option to specify real as opposed to lattice units
      • -
    -

    -examples

    -

    fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0

    -

    -description

    -

    Command to assign an id to a set of FE faces.

    -

    -restrictions

    -

    Only viable for rectangular grids.

    -

    -related

    -

    -default

    -

    The default option is units = lattice.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_create_nodeset.html b/doc/doc2/USER/atc/man_mesh_create_nodeset.html deleted file mode 100644 index 9d5d155654..0000000000 --- a/doc/doc2/USER/atc/man_mesh_create_nodeset.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_nodeset - - - - - - -
    - - -

    fix_modify AtC mesh create_nodeset

    -syntax

    -

    fix_modify AtC mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

    -
      -
    • <id> = id to assign to the collection of FE nodes
      • -
    • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes
      • -
    -

    -examples

    -

    fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12

    -

    -description

    -

    Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions.

    -

    -restrictions

    -

    -related

    -

    -default

    -

    Coordinates are assumed to be in lattice units.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_delete_elements.html b/doc/doc2/USER/atc/man_mesh_delete_elements.html deleted file mode 100644 index cc269c8e65..0000000000 --- a/doc/doc2/USER/atc/man_mesh_delete_elements.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC mesh delete_elements - - - - - - -
    - - -

    fix_modify AtC mesh delete_elements

    -syntax

    -

    fix_modify AtC mesh delete_elements <element_set>

    -
      -
    • <element_set> = name of an element set
      • -
    -

    -examples

    -

    fix_modify AtC delete_elements gap

    -

    -description

    -

    Deletes a group of elements from the mesh.

    -

    -restrictions

    -

    -related

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/doc2/USER/atc/man_mesh_nodeset_to_elementset.html deleted file mode 100644 index 45d03fc986..0000000000 --- a/doc/doc2/USER/atc/man_mesh_nodeset_to_elementset.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC mesh nodeset_to_elementset - - - - - - -
    - - -

    fix_modify AtC mesh nodeset_to_elementset

    -syntax

    -

    fix_modify AtC nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>

    -
      -
    • <nodeset_id> = id of desired nodeset from which to create elementset
      • -
    • <elementset_id> = id to assign to the collection of FE element
      • -
    • <max/min> = flag to choose either the maximal or minimal elementset
      • -
    -

    -examples

    -

    fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min

    -

    -description

    -

    Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created

    -

    -restrictions

    -

    None.

    -

    -related

    -

    -default

    -

    Unless specified, the maximal element set is created

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_output.html b/doc/doc2/USER/atc/man_mesh_output.html deleted file mode 100644 index be1b4c194f..0000000000 --- a/doc/doc2/USER/atc/man_mesh_output.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mesh output - - - - - - -
    - - -

    fix_modify AtC mesh output

    -syntax

    -

    fix_modify AtC mesh output <file_prefix>

    -

    -examples

    -

    fix_modify AtC mesh output meshData
    -

    -

    -description

    -

    Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data.

    -

    -restrictions

    -

    none

    -

    -related

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_quadrature.html b/doc/doc2/USER/atc/man_mesh_quadrature.html deleted file mode 100644 index d5291d99db..0000000000 --- a/doc/doc2/USER/atc/man_mesh_quadrature.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC mesh quadrature - - - - - - -
    - - -

    fix_modify AtC mesh quadrature

    -syntax

    -

    fix_modify AtC mesh quadrature <quad>

    -
      -
    • quad = one of <nodal|gauss1|gauss2|gauss3|face> --- when a mesh is created it defaults to gauss2, use this call to change it after the fact
      • -
    -

    -examples

    -

    fix_modify AtC mesh quadrature face

    -

    -description

    -

    (Re-)assigns the quadrature style for the existing mesh.

    -

    -restrictions

    -

    -related

    -

    fix_modify AtC mesh create

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_read.html b/doc/doc2/USER/atc/man_mesh_read.html deleted file mode 100644 index a497a2ed04..0000000000 --- a/doc/doc2/USER/atc/man_mesh_read.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC mesh read - - - - - - -
    - - -

    fix_modify AtC mesh read

    -syntax

    -

    fix_modify AtC mesh read <filename> <f|p> <f|p> <f|p>

    -
      -
    • filename = name of file containing mesh to be read
      • -
    • f p p = periodicity flags for x, y, z
      • -
    -

    -examples

    -

    fix_modify AtC mesh read myComponent.mesh p p p
    - fix_modify AtC mesh read myOtherComponent.exo

    -

    -description

    -

    Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed.

    -

    -restrictions

    -

    -related

    -

    -default

    -

    periodicity flags are false by default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_mesh_write.html b/doc/doc2/USER/atc/man_mesh_write.html deleted file mode 100644 index 21754a1e68..0000000000 --- a/doc/doc2/USER/atc/man_mesh_write.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC mesh write - - - - - - -
    - - -

    fix_modify AtC mesh write

    -syntax

    -

    fix_modify AtC mesh write <filename>

    -
      -
    • filename = name of file to write mesh
      • -
    -

    -examples

    -

    fix_modify AtC mesh write myMesh.mesh
    -

    -

    -description

    -

    Writes a mesh to a text file.

    -

    -restrictions

    -

    -related

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_momentum_time_integration.html b/doc/doc2/USER/atc/man_momentum_time_integration.html deleted file mode 100644 index 3b987f70ef..0000000000 --- a/doc/doc2/USER/atc/man_momentum_time_integration.html +++ /dev/null @@ -1,60 +0,0 @@ - - - - -ATC: fix_modify AtC time_integration (momentum) - - - - - - -
    - - -

    fix_modify AtC time_integration (momentum)

    -syntax

    -

    fix_modify AtC time_integration <descriptor>
    -

    -
      -
    • descriptor (string) = time integration type
      -
      • -
    -

    various time integration methods for the finite elements
    -

    -

    -description

    -

    verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force
    - fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes
    - gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power
    -

    -

    -examples

    -

    fix_modify atc time_integration verlet
    - fix_modify atc time_integration fractional_step
    -

    -

    -description

    -

    -related

    -

    see fix atc command

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_output.html b/doc/doc2/USER/atc/man_output.html deleted file mode 100644 index 3129ff30c9..0000000000 --- a/doc/doc2/USER/atc/man_output.html +++ /dev/null @@ -1,63 +0,0 @@ - - - - -ATC: fix_modify AtC output - - - - - - -
    - - -

    fix_modify AtC output

    -syntax

    -

    fix_modify AtC output <filename_prefix> <frequency> [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]

    -
      -
    • filename_prefix (string) = prefix for data files
      • -
    • frequency (integer) = frequency of output in time-steps
      • -
    • options (keyword/s):
      - text = creates text output of index, step and nodal variable values for unique nodes
      - full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes
      - binary = creates binary Ensight output
      - vector_components = outputs vectors as scalar components
      - tensor_components = outputs tensor as scalar components (use this for Paraview)
      -
      • -
    -

    -examples

    -

    fix_modify AtC output heatFE 100
    - fix_modify AtC output hardyFE 1 text tensor_components
    - fix_modify AtC output hardyFE 10 text binary tensor_components
    - fix_modify AtC output index step
    -

    -

    -description

    -

    Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible.

    -

    -restrictions

    -

    -related

    -

    see fix atc command

    -

    -default

    -

    no default format output indexed by time

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_output_elementset.html b/doc/doc2/USER/atc/man_output_elementset.html deleted file mode 100644 index be259388ba..0000000000 --- a/doc/doc2/USER/atc/man_output_elementset.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC output elementset - - - - - - -
    - - -

    fix_modify AtC output elementset

    -syntax

    -

    fix_modify AtC output volume_integral <eset_name> <field> {`

    -
      -
    • set_name (string) = name of elementset to be integrated over
      • -
    • fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset
      -
      • -
    -

    -examples

    -

    fix_modify AtC output eset1 mass_density
    -

    -

    -description

    -

    Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file.

    -

    -restrictions

    -

    -related

    -

    see fix atc command

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_output_nodeset.html b/doc/doc2/USER/atc/man_output_nodeset.html deleted file mode 100644 index db76c8008e..0000000000 --- a/doc/doc2/USER/atc/man_output_nodeset.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - -ATC: fix_modify AtC output nodeset - - - - - - -
    - - -

    fix_modify AtC output nodeset

    -syntax

    -

    fix_modify AtC output nodeset <nodeset_name> <operation>

    -
      -
    • nodeset_name (string) = name of nodeset to be operated on
      • -
    • operation (keyword/s):
      - sum = creates nodal sum over nodes in specified nodeset
      -
      • -
    -

    -examples

    -

    fix_modify AtC output nodeset nset1 sum
    -

    -

    -description

    -

    Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file.

    -

    -restrictions

    -

    -related

    -

    see fix atc command

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_pair_interactions.html b/doc/doc2/USER/atc/man_pair_interactions.html deleted file mode 100644 index d46dcb1234..0000000000 --- a/doc/doc2/USER/atc/man_pair_interactions.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC pair_interactions/bond_interactions - - - - - - -
    - - -

    fix_modify AtC pair_interactions/bond_interactions

    -syntax

    -

    fix_modify AtC pair_interactions <on|off>
    - fix_modify AtC bond_interactions <on|off>
    -

    -

    -examples

    -

    fix_modify AtC bond_interactions on
    -

    -

    -description

    -

    include bonds and/or pairs in the stress and heat flux computations

    -

    -restrictions

    -

    -related

    -

    -default

    -

    pair interactions: on, bond interactions: off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_poisson_solver.html b/doc/doc2/USER/atc/man_poisson_solver.html deleted file mode 100644 index d69d74db1a..0000000000 --- a/doc/doc2/USER/atc/man_poisson_solver.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC poisson_solver - - - - - - -
    - - -

    fix_modify AtC poisson_solver

    -syntax

    -

    fix_modify AtC poisson_solver mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>

    -
      -
    • nx ny nz = number of elements in x, y, z
      • -
    • region-id = id of region that is to be meshed
      • -
    • f p p = perioidicity flags for x, y, z
      • -
    -

    -examples

    -

    fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p

    -

    -description

    -

    Creates a uniform mesh in a rectangular region

    -

    -restrictions

    -

    creates only uniform rectangular grids in a rectangular region

    -

    -related

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_read_restart.html b/doc/doc2/USER/atc/man_read_restart.html deleted file mode 100644 index 96168fccc7..0000000000 --- a/doc/doc2/USER/atc/man_read_restart.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC read_restart - - - - - - -
    - - -

    fix_modify AtC read_restart

    -syntax

    -

    fix_modify AtC read_restart [file_name]
    -

    -

    -examples

    -

    fix_modify AtC read_restart ATC_state
    -

    -

    -description

    -

    Reads the current state of the fields from a named text-based restart file.

    -

    -restrictions

    -

    The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.

    -

    -related

    -

    see write_restart fix_modify AtC write_restart

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_remove_molecule.html b/doc/doc2/USER/atc/man_remove_molecule.html deleted file mode 100644 index 054291efda..0000000000 --- a/doc/doc2/USER/atc/man_remove_molecule.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC remove_molecule - - - - - - -
    - - -

    fix_modify AtC remove_molecule

    -syntax

    -

    fix_modify_AtC remove_molecule <TAG>
    -

    -
      -
    • <TAG> = tag for tracking a molecule type
      -
      • -
    -

    -examples

    -

    fix_modify AtC remove_molecule water
    -

    -

    -description

    -

    Removes tag designated for tracking a specified set of molecules.
    -

    -

    -restrictions

    -

    -related

    -

    -default

    -

    No defaults for this command.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_remove_source.html b/doc/doc2/USER/atc/man_remove_source.html deleted file mode 100644 index d1d249eb76..0000000000 --- a/doc/doc2/USER/atc/man_remove_source.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC remove_source - - - - - - -
    - - -

    fix_modify AtC remove_source

    -syntax

    -

    fix_modify AtC remove_source <field> <element_set>

    -
      -
    • <field> = field name valid for type of physics
      • -
    • <element_set> = name of set of elements
      • -
    -

    -examples

    -

    fix_modify atc remove_source temperature groupNAME

    -

    -description

    -

    Remove a domain source.

    -

    -restrictions

    -

    keyword 'all' reserved in element_set name

    -

    -related

    -

    see fix_modify AtC source

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_remove_species.html b/doc/doc2/USER/atc/man_remove_species.html deleted file mode 100644 index ba94a52658..0000000000 --- a/doc/doc2/USER/atc/man_remove_species.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC remove_species - - - - - - -
    - - -

    fix_modify AtC remove_species

    -syntax

    -

    fix_modify_AtC delete_species <TAG>
    -

    -
      -
    • <TAG> = tag for tracking a species
      -
      • -
    -

    -examples

    -

    fix_modify AtC remove_species gold
    -

    -

    -description

    -

    Removes tag designated for tracking a specified species.
    -

    -

    -restrictions

    -

    -related

    -

    -default

    -

    No defaults for this command.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_reset_atomic_reference_positions.html b/doc/doc2/USER/atc/man_reset_atomic_reference_positions.html deleted file mode 100644 index cb82f61bbb..0000000000 --- a/doc/doc2/USER/atc/man_reset_atomic_reference_positions.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC reset_atomic_reference_positions - - - - - - -
    - - -

    fix_modify AtC reset_atomic_reference_positions

    -syntax

    -

    fix_modify AtC reset_atomic_reference_positions

    -

    -examples

    -

    fix_modify atc reset_atomic_reference_positions

    -

    -description

    -

    Resets the atomic positions ATC uses to perform point to field operations. In can be used to use perfect lattice sites in ATC but a thermalized or deformed lattice in LAMMPS.

    -

    -restrictions

    -

    -

    -related

    -

    -

    -default

    -

    Default is off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_reset_time.html b/doc/doc2/USER/atc/man_reset_time.html deleted file mode 100644 index 35d75ccb97..0000000000 --- a/doc/doc2/USER/atc/man_reset_time.html +++ /dev/null @@ -1,65 +0,0 @@ - - - - -ATC: fix_modify AtC reset_time - - - - - - -
    - - -

    fix_modify AtC reset_time

    -syntax

    -

    fix_modify AtC reset_time

    -

    -examples

    -

    fix_modify atc reset_time 0.0
    -

    -

    -description

    -

    Resets the simulation time counter.

    -

    -restrictions

    -

    -related

    -

    -default

    -

    -syntax

    -

    fix_modify AtC kernel_bandwidth

    -

    -examples

    -

    fix_modify atc reset_time 8
    -

    -

    -description

    -

    Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations.

    -

    -restrictions

    -

    Only is used if kernel functions are being used.

    -

    -related

    -

    -default

    -

    Number of sample locations.

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_sample_frequency.html b/doc/doc2/USER/atc/man_sample_frequency.html deleted file mode 100644 index 13f468b222..0000000000 --- a/doc/doc2/USER/atc/man_sample_frequency.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC sample_frequency - - - - - - -
    - - -

    fix_modify AtC sample_frequency

    -syntax

    -

    fix_modify AtC sample_frequency [freq]

    -
      -
    • freq (int) : frequency to sample field in number of steps
      • -
    -

    -examples

    -

    fix_modify AtC sample_frequency 10

    -

    -description

    -

    Specifies a frequency at which fields are computed for the case where time filters are being applied.

    -

    -restrictions

    -

    Must be used with the hardy/field AtC fix ( see fix atc command ) and is only relevant when time filters are being used.

    -

    -related

    -

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_set.html b/doc/doc2/USER/atc/man_set.html deleted file mode 100644 index d104e535b6..0000000000 --- a/doc/doc2/USER/atc/man_set.html +++ /dev/null @@ -1,56 +0,0 @@ - - - - -ATC: fix_modify AtC set - - - - - - -
    - - -

    fix_modify AtC set

    -syntax

    -

    fix_modify AtC set reference_potential_energy <value_or_filename(optional)>

    -
      -
    • value (double) : optional user specified zero point for PE in native LAMMPS energy units
      -
      • -
    • filename (string) : optional user specified string for file of nodal PE values to be read-in
      • -
    -

    -examples

    -

    fix_modify AtC set reference_potential_energy
    - fix_modify AtC set reference_potential_energy -0.05
    - fix_modify AtC set reference_potential_energy myPEvalues
    -

    -

    -description

    -

    Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename.

    -

    -restrictions

    -

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    -

    -related

    -

    -default

    -

    Defaults to lammps zero point i.e. isolated atoms

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_source.html b/doc/doc2/USER/atc/man_source.html deleted file mode 100644 index 833b2a866f..0000000000 --- a/doc/doc2/USER/atc/man_source.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC source - - - - - - -
    - - -

    fix_modify AtC source

    -syntax

    -

    fix_modify AtC source <field> <element_set> <value | function>

    -
      -
    • <field> = field name valid for type of physics
      • -
    • <element_set> = name of set of elements
      • -
    -

    -examples

    -

    fix_modify atc source temperature middle temporal_ramp 10. 0.

    -

    -description

    -

    Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time.

    -

    -restrictions

    -

    keyword 'all' reserved in element_set name

    -

    -related

    -

    see fix_modify AtC remove_source

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_source_integration.html b/doc/doc2/USER/atc/man_source_integration.html deleted file mode 100644 index 70f62d2e57..0000000000 --- a/doc/doc2/USER/atc/man_source_integration.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC source_integration - - - - - - -
    - - -

    fix_modify AtC source_integration

    -syntax

    -

    fix_modify AtC source_integration < fe | atom>

    -

    -examples

    -

    fix_modify atc source_integration atom

    -

    -description

    -

    -restrictions

    -

    -related

    -

    -default

    -

    Default is fe

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_temperature_definition.html b/doc/doc2/USER/atc/man_temperature_definition.html deleted file mode 100644 index f4fb21471c..0000000000 --- a/doc/doc2/USER/atc/man_temperature_definition.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC temperature_definition - - - - - - -
    - - -

    fix_modify AtC temperature_definition

    -syntax

    -

    fix_modify AtC temperature_definition <kinetic|total>

    -

    -examples

    -

    fix_modify atc temperature_definition kinetic
    -

    -

    -description

    -

    Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.

    -

    -restrictions

    -

    This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.

    -

    -default

    -

    kinetic

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_thermal_time_integration.html b/doc/doc2/USER/atc/man_thermal_time_integration.html deleted file mode 100644 index c2f636134f..0000000000 --- a/doc/doc2/USER/atc/man_thermal_time_integration.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - -ATC: fix_modify AtC time_integration (thermal) - - - - - - -
    - - -

    fix_modify AtC time_integration (thermal)

    -syntax

    -

    fix_modify AtC time_integration <descriptor>
    -

    -
      -
    • descriptor (string) = time integration type
      -
      • -
    -

    various time integration methods for the finite elements
    -

    -

    -description

    -

    gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power
    - fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes
    -

    -

    -examples

    -

    fix_modify atc time_integration gear
    - fix_modify atc time_integration fractional_step
    -

    -

    -description

    -

    -related

    -

    see fix atc command

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_time_filter.html b/doc/doc2/USER/atc/man_time_filter.html deleted file mode 100644 index ec70fed871..0000000000 --- a/doc/doc2/USER/atc/man_time_filter.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC filter - - - - - - -
    - - -

    fix_modify AtC filter

    -syntax

    -

    fix_modify AtC filter <on | off | equilibrate>
    -

    -
      -
    • on | off (keyword) = turns filter on or off
      -
      • -
    • equilibrate = runs dynamics without filtering but initializes filtered quantities
      • -
    -

    -examples

    -

    fix_modify atc transfer filter on
    -

    -

    -description

    -

    Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics

    -

    -restrictions

    -

    only for be used with specific transfers: thermal, two_temperature

    -

    -related

    -

    fix_modify AtC filter scale
    - fix_modify AtC equilibrium_start

    -

    -default

    -

    off

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_track_displacement.html b/doc/doc2/USER/atc/man_track_displacement.html deleted file mode 100644 index 8f729cffe3..0000000000 --- a/doc/doc2/USER/atc/man_track_displacement.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC track_displacement - - - - - - -
    - - -

    fix_modify AtC track_displacement

    -syntax

    -

    fix_modify AtC track_displacement <on/off>
    -

    -

    -examples

    -

    fix_modify atc track_displacement on
    -

    -

    -description

    -

    Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.

    -

    -restrictions

    -

    Some constitutive models require the displacement field

    -

    -default

    -

    on

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_unfix_flux.html b/doc/doc2/USER/atc/man_unfix_flux.html deleted file mode 100644 index b2a19a7fd0..0000000000 --- a/doc/doc2/USER/atc/man_unfix_flux.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC unfix_flux - - - - - - -
    - - -

    fix_modify AtC unfix_flux

    -syntax

    -

    fix_modify AtC fix_flux <field> <face_set> <value | function>

    -
      -
    • <field> = field name valid for type of physics, temperature | electron_temperature
      • -
    • <face_set> = name of set of element faces
      • -
    -

    -examples

    -

    fix_modify atc unfix_flux temperature faceSet
    -

    -

    -description

    -

    Command for removing prescribed normal fluxes e.g. heat_flux, stress.

    -

    -restrictions

    -

    -related

    -

    see fix_modify AtC unfix_flux

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_unfix_nodes.html b/doc/doc2/USER/atc/man_unfix_nodes.html deleted file mode 100644 index 498d549f9e..0000000000 --- a/doc/doc2/USER/atc/man_unfix_nodes.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC unfix - - - - - - -
    - - -

    fix_modify AtC unfix

    -syntax

    -

    fix_modify AtC unfix <field> <nodeset>

    -
      -
    • <field> = field name valid for type of physics
      • -
    • <nodeset> = name of set of nodes
      • -
    -

    -examples

    -

    fix_modify AtC unfix temperature groupNAME

    -

    -description

    -

    Removes constraint on field values for specified nodes.

    -

    -restrictions

    -

    keyword 'all' reserved in nodeset name

    -

    -related

    -

    see fix_modify AtC fix

    -

    -default

    -

    none

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_write_atom_weights.html b/doc/doc2/USER/atc/man_write_atom_weights.html deleted file mode 100644 index 939506a28e..0000000000 --- a/doc/doc2/USER/atc/man_write_atom_weights.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC write_atom_weights - - - - - - -
    - - -

    fix_modify AtC write_atom_weights

    -syntax

    -

    fix_modify AtC write_atom_weights <filename> <frequency>

    -
      -
    • <filename> = name of file that atomic weights are written to
      -
      • -
    • <frequency> = how often writes will occur
      -
      • -
    -

    -examples

    -

    fix_modify atc write_atom_weights atm_wt_file.txt 10
    -

    -

    -description

    -

    Command for writing the values of atomic weights to a specified file.

    -

    -restrictions

    -

    -related

    -

    -default

    -
    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/USER/atc/man_write_restart.html b/doc/doc2/USER/atc/man_write_restart.html deleted file mode 100644 index 6ea350d5e8..0000000000 --- a/doc/doc2/USER/atc/man_write_restart.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC write_restart - - - - - - -
    - - -

    fix_modify AtC write_restart

    -syntax

    -

    fix_modify AtC write_restart [file_name]
    -

    -

    -examples

    -

    fix_modify AtC write_restart restart.mydata
    -

    -

    -description

    -

    Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command.

    -

    -restrictions

    -

    The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.

    -

    -related

    -

    see read_restart fix_modify AtC read_restart

    -

    -default

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    none

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    -
    Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
    - - diff --git a/doc/doc2/accelerate_cuda.html b/doc/doc2/accelerate_cuda.html deleted file mode 100644 index 0f3017b09b..0000000000 --- a/doc/doc2/accelerate_cuda.html +++ /dev/null @@ -1,228 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    Return to Section accelerate overview -

    -

    5.3.1 USER-CUDA package -

    -

    The USER-CUDA package was developed by Christian Trott (Sandia) while -at U Technology Ilmenau in Germany. It provides NVIDIA GPU versions -of many pair styles, many fixes, a few computes, and for long-range -Coulombics via the PPPM command. It has the following general -features: -

    -
    • The package is designed to allow an entire LAMMPS calculation, for -many timesteps, to run entirely on the GPU (except for inter-processor -MPI communication), so that atom-based data (e.g. coordinates, forces) -do not have to move back-and-forth between the CPU and GPU. - -
    • The speed-up advantage of this approach is typically better when the -number of atoms per GPU is large - -
    • Data will stay on the GPU until a timestep where a non-USER-CUDA fix -or compute is invoked. Whenever a non-GPU operation occurs (fix, -compute, output), data automatically moves back to the CPU as needed. -This may incur a performance penalty, but should otherwise work -transparently. - -
    • Neighbor lists are constructed on the GPU. - -
    • The package only supports use of a single MPI task, running on a -single CPU (core), assigned to each GPU. -
    -

    Here is a quick overview of how to use the USER-CUDA package: -

    -
    • build the library in lib/cuda for your GPU hardware with desired precision -
    • include the USER-CUDA package and build LAMMPS -
    • use the mpirun command to specify 1 MPI task per GPU (on each node) -
    • enable the USER-CUDA package via the "-c on" command-line switch -
    • specify the # of GPUs per node -
    • use USER-CUDA styles in your input script -
    -

    The latter two steps can be done using the "-pk cuda" and "-sf cuda" -command-line switches respectively. Or -the effect of the "-pk" or "-sf" switches can be duplicated by adding -the package cuda or suffix cuda commands -respectively to your input script. -

    -

    Required hardware/software: -

    -

    To use this package, you need to have one or more NVIDIA GPUs and -install the NVIDIA Cuda software on your system: -

    -

    Your NVIDIA GPU needs to support Compute Capability 1.3. This list may -help you to find out the Compute Capability of your card: -

    -

    http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units -

    -

    Install the Nvidia Cuda Toolkit (version 3.2 or higher) and the -corresponding GPU drivers. The Nvidia Cuda SDK is not required, but -we recommend it also be installed. You can then make sure its sample -projects can be compiled without problems. -

    -

    Building LAMMPS with the USER-CUDA package: -

    -

    This requires two steps (a,b): build the USER-CUDA library, then build -LAMMPS with the USER-CUDA package. -

    -

    You can do both these steps in one line, using the src/Make.py script, -described in Section 2.4 of the manual. -Type "Make.py -h" for help. If run from the src directory, this -command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the -starting Makefile.machine: -

    -
    Make.py -p cuda -cuda mode=single arch=20 -o cuda -a lib-cuda file mpi 
-
    -

    Or you can follow these two (a,b) steps: -

    -

    (a) Build the USER-CUDA library -

    -

    The USER-CUDA library is in lammps/lib/cuda. If your CUDA toolkit -is not installed in the default system directoy /usr/local/cuda edit -the file lib/cuda/Makefile.common accordingly. -

    -

    To build the library with the settings in lib/cuda/Makefile.default, -simply type: -

    -
    make 
-
    -

    To set options when the library is built, type "make OPTIONS", where -OPTIONS are one or more of the following. The settings will be -written to the lib/cuda/Makefile.defaults before the build. -

    -
    precision=N to set the precision level
-  N = 1 for single precision (default)
-  N = 2 for double precision
-  N = 3 for positions in double precision
-  N = 4 for positions and velocities in double precision
-arch=M to set GPU compute capability
-  M = 35 for Kepler GPUs
-  M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) (default)
-  M = 21 for CC2.1 (GF104/114,  e.g. GTX560, GTX460, GTX450)
-  M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
-prec_timer=0/1 to use hi-precision timers
-  0 = do not use them (default)
-  1 = use them
-  this is usually only useful for Mac machines 
-dbg=0/1 to activate debug mode
-  0 = no debug mode (default)
-  1 = yes debug mode
-  this is only useful for developers
-cufft=1 for use of the CUDA FFT library
-  0 = no CUFFT support (default)
-  in the future other CUDA-enabled FFT libraries might be supported 
-
    -

    If the build is successful, it will produce the files liblammpscuda.a and -Makefile.lammps. -

    -

    Note that if you change any of the options (like precision), you need -to re-build the entire library. Do a "make clean" first, followed by -"make". -

    -

    (b) Build LAMMPS with the USER-CUDA package -

    -
    cd lammps/src
-make yes-user-cuda
-make machine 
-
    -

    No additional compile/link flags are needed in Makefile.machine. -

    -

    Note that if you change the USER-CUDA library precision (discussed -above) and rebuild the USER-CUDA library, then you also need to -re-install the USER-CUDA package and re-build LAMMPS, so that all -affected files are re-compiled and linked to the new USER-CUDA -library. -

    -

    Run with the USER-CUDA package from the command line: -

    -

    The mpirun or mpiexec command sets the total number of MPI tasks used -by LAMMPS (one or multiple per compute node) and the number of MPI -tasks used per node. E.g. the mpirun command in MPICH does this via -its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. -

    -

    When using the USER-CUDA package, you must use exactly one MPI task -per physical GPU. -

    -

    You must use the "-c on" command-line -switch to enable the USER-CUDA package. -The "-c on" switch also issues a default package cuda 1 -command which sets various USER-CUDA options to default values, as -discussed on the package command doc page. -

    -

    Use the "-sf cuda" command-line switch, -which will automatically append "cuda" to styles that support it. Use -the "-pk cuda Ng" command-line switch to -set Ng = # of GPUs per node to a different value than the default set -by the "-c on" switch (1 GPU) or change other package -cuda options. -

    -
    lmp_machine -c on -sf cuda -pk cuda 1 -in in.script                       # 1 MPI task uses 1 GPU
-mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script          # 2 MPI tasks use 2 GPUs on a single 16-core (or whatever) node
-mpirun -np 24 -ppn 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script  # ditto on 12 16-core nodes 
-
    -

    The syntax for the "-pk" switch is the same as same as the "package -cuda" command. See the package command doc page for -details, including the default values used for all its options if it -is not specified. -

    -

    Note that the default for the package cuda command is -to set the Newton flag to "off" for both pairwise and bonded -interactions. This typically gives fastest performance. If the -newton command is used in the input script, it can -override these defaults. -

    -

    Or run with the USER-CUDA package by editing an input script: -

    -

    The discussion above for the mpirun/mpiexec command and the requirement -of one MPI task per GPU is the same. -

    -

    You must still use the "-c on" command-line -switch to enable the USER-CUDA package. -

    -

    Use the suffix cuda command, or you can explicitly add a -"cuda" suffix to individual styles in your input script, e.g. -

    -
    pair_style lj/cut/cuda 2.5 
-
    -

    You only need to use the package cuda command if you -wish to change any of its option defaults, including the number of -GPUs/node (default = 1), as set by the "-c on" command-line -switch. -

    -

    Speed-ups to expect: -

    -

    The performance of a GPU versus a multi-core CPU is a function of your -hardware, which pair style is used, the number of atoms/GPU, and the -precision used on the GPU (double, single, mixed). -

    -

    See the Benchmark page of the -LAMMPS web site for performance of the USER-CUDA package on different -hardware. -

    -

    Guidelines for best performance: -

    -
    • The USER-CUDA package offers more speed-up relative to CPU performance -when the number of atoms per GPU is large, e.g. on the order of tens -or hundreds of 1000s. - -
    • As noted above, this package will continue to run a simulation -entirely on the GPU(s) (except for inter-processor MPI communication), -for multiple timesteps, until a CPU calculation is required, either by -a fix or compute that is non-GPU-ized, or until output is performed -(thermo or dump snapshot or restart file). The less often this -occurs, the faster your simulation will run. -
    -

    Restrictions: -

    -

    None. -

    - diff --git a/doc/doc2/accelerate_gpu.html b/doc/doc2/accelerate_gpu.html deleted file mode 100644 index b8f2f6705f..0000000000 --- a/doc/doc2/accelerate_gpu.html +++ /dev/null @@ -1,257 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    Return to Section accelerate overview -

    -

    5.3.2 GPU package -

    -

    The GPU package was developed by Mike Brown at ORNL and his -collaborators, particularly Trung Nguyen (ORNL). It provides GPU -versions of many pair styles, including the 3-body Stillinger-Weber -pair style, and for kspace_style pppm for -long-range Coulombics. It has the following general features: -

    -
    • It is designed to exploit common GPU hardware configurations where one -or more GPUs are coupled to many cores of one or more multi-core CPUs, -e.g. within a node of a parallel machine. - -
    • Atom-based data (e.g. coordinates, forces) moves back-and-forth -between the CPU(s) and GPU every timestep. - -
    • Neighbor lists can be built on the CPU or on the GPU - -
    • The charge assignement and force interpolation portions of PPPM can be -run on the GPU. The FFT portion, which requires MPI communication -between processors, runs on the CPU. - -
    • Asynchronous force computations can be performed simultaneously on the -CPU(s) and GPU. - -
    • It allows for GPU computations to be performed in single or double -precision, or in mixed-mode precision, where pairwise forces are -computed in single precision, but accumulated into double-precision -force vectors. - -
    • LAMMPS-specific code is in the GPU package. It makes calls to a -generic GPU library in the lib/gpu directory. This library provides -NVIDIA support as well as more general OpenCL support, so that the -same functionality can eventually be supported on a variety of GPU -hardware. -
    -

    Here is a quick overview of how to use the GPU package: -

    -
    • build the library in lib/gpu for your GPU hardware wity desired precision -
    • include the GPU package and build LAMMPS -
    • use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU -
    • specify the # of GPUs per node -
    • use GPU styles in your input script -
    -

    The latter two steps can be done using the "-pk gpu" and "-sf gpu" -command-line switches respectively. Or -the effect of the "-pk" or "-sf" switches can be duplicated by adding -the package gpu or suffix gpu commands -respectively to your input script. -

    -

    Required hardware/software: -

    -

    To use this package, you currently need to have an NVIDIA GPU and -install the NVIDIA Cuda software on your system: -

    -
    • Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information -
    • Go to http://www.nvidia.com/object/cuda_get.html -
    • Install a driver and toolkit appropriate for your system (SDK is not necessary) -
    • Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties -
    -

    Building LAMMPS with the GPU package: -

    -

    This requires two steps (a,b): build the GPU library, then build -LAMMPS with the GPU package. -

    -

    You can do both these steps in one line, using the src/Make.py script, -described in Section 2.4 of the manual. -Type "Make.py -h" for help. If run from the src directory, this -command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the -starting Makefile.machine: -

    -
    Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi 
-
    -

    Or you can follow these two (a,b) steps: -

    -

    (a) Build the GPU library -

    -

    The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in -lib/gpu) appropriate for your system. You should pay special -attention to 3 settings in this makefile. -

    -
    • CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system -
    • CUDA_ARCH = needs to be appropriate to your GPUs -
    • CUDA_PREC = precision (double, mixed, single) you desire -
    -

    See lib/gpu/Makefile.linux.double for examples of the ARCH settings -for different GPU choices, e.g. Fermi vs Kepler. It also lists the -possible precision settings: -

    -
    CUDA_PREC = -D_SINGLE_SINGLE  # single precision for all calculations
-CUDA_PREC = -D_DOUBLE_DOUBLE  # double precision for all calculations
-CUDA_PREC = -D_SINGLE_DOUBLE  # accumulation of forces, etc, in double 
-
    -

    The last setting is the mixed mode referred to above. Note that your -GPU must support double precision to use either the 2nd or 3rd of -these settings. -

    -

    To build the library, type: -

    -
    make -f Makefile.machine 
-
    -

    If successful, it will produce the files libgpu.a and Makefile.lammps. -

    -

    The latter file has 3 settings that need to be appropriate for the -paths and settings for the CUDA system software on your machine. -Makefile.lammps is a copy of the file specified by the EXTRAMAKE -setting in Makefile.machine. You can change EXTRAMAKE or create your -own Makefile.lammps.machine if needed. -

    -

    Note that to change the precision of the GPU library, you need to -re-build the entire library. Do a "clean" first, e.g. "make -f -Makefile.linux clean", followed by the make command above. -

    -

    (b) Build LAMMPS with the GPU package -

    -
    cd lammps/src
-make yes-gpu
-make machine 
-
    -

    No additional compile/link flags are needed in Makefile.machine. -

    -

    Note that if you change the GPU library precision (discussed above) -and rebuild the GPU library, then you also need to re-install the GPU -package and re-build LAMMPS, so that all affected files are -re-compiled and linked to the new GPU library. -

    -

    Run with the GPU package from the command line: -

    -

    The mpirun or mpiexec command sets the total number of MPI tasks used -by LAMMPS (one or multiple per compute node) and the number of MPI -tasks used per node. E.g. the mpirun command in MPICH does this via -its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. -

    -

    When using the GPU package, you cannot assign more than one GPU to a -single MPI task. However multiple MPI tasks can share the same GPU, -and in many cases it will be more efficient to run this way. Likewise -it may be more efficient to use less MPI tasks/node than the available -# of CPU cores. Assignment of multiple MPI tasks to a GPU will happen -automatically if you create more MPI tasks/node than there are -GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be -shared by 4 MPI tasks. -

    -

    Use the "-sf gpu" command-line switch, -which will automatically append "gpu" to styles that support it. Use -the "-pk gpu Ng" command-line switch to -set Ng = # of GPUs/node to use. -

    -
    lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
-mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script           # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
-mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes 
-
    -

    Note that if the "-sf gpu" switch is used, it also issues a default -package gpu 1 command, which sets the number of -GPUs/node to 1. -

    -

    Using the "-pk" switch explicitly allows for setting of the number of -GPUs/node to use and additional options. Its syntax is the same as -same as the "package gpu" command. See the package -command doc page for details, including the default values used for -all its options if it is not specified. -

    -

    Note that the default for the package gpu command is to -set the Newton flag to "off" pairwise interactions. It does not -affect the setting for bonded interactions (LAMMPS default is "on"). -The "off" setting for pairwise interaction is currently required for -GPU package pair styles. -

    -

    Or run with the GPU package by editing an input script: -

    -

    The discussion above for the mpirun/mpiexec command, MPI tasks/node, -and use of multiple MPI tasks/GPU is the same. -

    -

    Use the suffix gpu command, or you can explicitly add an -"gpu" suffix to individual styles in your input script, e.g. -

    -
    pair_style lj/cut/gpu 2.5 
-
    -

    You must also use the package gpu command to enable the -GPU package, unless the "-sf gpu" or "-pk gpu" command-line -switches were used. It specifies the -number of GPUs/node to use, as well as other options. -

    -

    Speed-ups to expect: -

    -

    The performance of a GPU versus a multi-core CPU is a function of your -hardware, which pair style is used, the number of atoms/GPU, and the -precision used on the GPU (double, single, mixed). -

    -

    See the Benchmark page of the -LAMMPS web site for performance of the GPU package on various -hardware, including the Titan HPC platform at ORNL. -

    -

    You should also experiment with how many MPI tasks per GPU to use to -give the best performance for your problem and machine. This is also -a function of the problem size and the pair style being using. -Likewise, you should experiment with the precision setting for the GPU -library to see if single or mixed precision will give accurate -results, since they will typically be faster. -

    -

    Guidelines for best performance: -

    -
    • Using multiple MPI tasks per GPU will often give the best performance, -as allowed my most multi-core CPU/GPU configurations. - -
    • If the number of particles per MPI task is small (e.g. 100s of -particles), it can be more efficient to run with fewer MPI tasks per -GPU, even if you do not use all the cores on the compute node. - -
    • The package gpu command has several options for tuning -performance. Neighbor lists can be built on the GPU or CPU. Force -calculations can be dynamically balanced across the CPU cores and -GPUs. GPU-specific settings can be made which can be optimized -for different hardware. See the packakge command -doc page for details. - -
    • As described by the package gpu command, GPU -accelerated pair styles can perform computations asynchronously with -CPU computations. The "Pair" time reported by LAMMPS will be the -maximum of the time required to complete the CPU pair style -computations and the time required to complete the GPU pair style -computations. Any time spent for GPU-enabled pair styles for -computations that run simultaneously with bond, -angle, dihedral, -improper, and long-range -calculations will not be included in the "Pair" time. - -
    • When the mode setting for the package gpu command is force/neigh, -the time for neighbor list calculations on the GPU will be added into -the "Pair" time, not the "Neigh" time. An additional breakdown of the -times required for various tasks on the GPU (data copy, neighbor -calculations, force computations, etc) are output only with the LAMMPS -screen output (not in the log file) at the end of each run. These -timings represent total time spent on the GPU for each routine, -regardless of asynchronous CPU calculations. - -
    • The output section "GPU Time Info (average)" reports "Max Mem / Proc". -This is the maximum memory used at one time on the GPU for data -storage by a single MPI process. -
    -

    Restrictions: -

    -

    None. -

    - diff --git a/doc/doc2/accelerate_intel.html b/doc/doc2/accelerate_intel.html deleted file mode 100644 index 63c739f92a..0000000000 --- a/doc/doc2/accelerate_intel.html +++ /dev/null @@ -1,326 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    Return to Section accelerate overview -

    -

    5.3.3 USER-INTEL package -

    -

    The USER-INTEL package was developed by Mike Brown at Intel -Corporation. It provides two methods for accelerating simulations, -depending on the hardware you have. The first is acceleration on -Intel(R) CPUs by running in single, mixed, or double precision with -vectorization. The second is acceleration on Intel(R) Xeon Phi(TM) -coprocessors via offloading neighbor list and non-bonded force -calculations to the Phi. The same C++ code is used in both cases. -When offloading to a coprocessor from a CPU, the same routine is run -twice, once on the CPU and once with an offload flag. -

    -

    Note that the USER-INTEL package supports use of the Phi in "offload" -mode, not "native" mode like the KOKKOS -package. -

    -

    Also note that the USER-INTEL package can be used in tandem with the -USER-OMP package. This is useful when -offloading pair style computations to the Phi, so that other styles -not supported by the USER-INTEL package, e.g. bond, angle, dihedral, -improper, and long-range electrostatics, can run simultaneously in -threaded mode on the CPU cores. Since less MPI tasks than CPU cores -will typically be invoked when running with coprocessors, this enables -the extra CPU cores to be used for useful computation. -

    -

    As illustrated below, if LAMMPS is built with both the USER-INTEL and -USER-OMP packages, this dual mode of operation is made easier to use, -via the "-suffix hybrid intel omp" command-line -switch or the suffix hybrid intel -omp command. Both set a second-choice suffix to "omp" so -that styles from the USER-INTEL package will be used if available, -with styles from the USER-OMP package as a second choice. -

    -

    Here is a quick overview of how to use the USER-INTEL package for CPU -acceleration, assuming one or more 16-core nodes. More details -follow. -

    -
    use an Intel compiler
-use these CCFLAGS settings in Makefile.machine: -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
-use these LINKFLAGS settings in Makefile.machine: -fopenmp, -xHost
-make yes-user-intel yes-user-omp     # including user-omp is optional
-make mpi                             # build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi
-make intel_cpu                       # or Makefile.intel_cpu already has settings, uses Intel MPI wrapper
-Make.py -v -p intel omp -intel cpu -a file mpich_icc   # or one-line build via Make.py for MPICH
-Make.py -v -p intel omp -intel cpu -a file ompi_icc    # or for OpenMPI
-Make.py -v -p intel omp -intel cpu -a file intel_cpu   # or for Intel MPI wrapper 
-
    -
    lmp_machine -sf intel -pk intel 0 omp 16 -in in.script    # 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP
-mpirun -np 32 lmp_machine -sf intel -in in.script         # 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP
-lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -pk omp 16 -in in.script         # 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP
-mpirun -np 32 -ppn 4 lmp_machine -sf hybrid intel omp -pk omp 4 -pk omp 4 -in in.script      # 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP 
-
    -

    Here is a quick overview of how to use the USER-INTEL package for the -same CPUs as above (16 cores/node), with an additional Xeon Phi(TM) -coprocessor per node. More details follow. -

    -
    Same as above for building, with these additions/changes:
-add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in Makefile.machine
-add the flag -offload to LINKFLAGS in Makefile.machine
-for Make.py change "-intel cpu" to "-intel phi", and "file intel_cpu" to "file intel_phi" 
-
    -
    mpirun -np 32 lmp_machine -sf intel -pk intel 1 -in in.script                 # 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP
-mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script            # 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP
-mpirun -np 32 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -pk omp 2 -in in.script # 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP 
-
    -

    Required hardware/software: -

    -

    Your compiler must support the OpenMP interface. Use of an Intel(R) -C++ compiler is recommended, but not required. However, g++ will not -recognize some of the settings listed above, so they cannot be used. -Optimizations for vectorization have only been tested with the -Intel(R) compiler. Use of other compilers may not result in -vectorization, or give poor performance. -

    -

    The recommended version of the Intel(R) compiler is 14.0.1.106. -Versions 15.0.1.133 and later are also supported. If using Intel(R) -MPI, versions 15.0.2.044 and later are recommended. -

    -

    To use the offload option, you must have one or more Intel(R) Xeon -Phi(TM) coprocessors and use an Intel(R) C++ compiler. -

    -

    Building LAMMPS with the USER-INTEL package: -

    -

    The lines above illustrate how to include/build with the USER-INTEL -package, for either CPU or Phi support, in two steps, using the "make" -command. Or how to do it with one command via the src/Make.py script, -described in Section 2.4 of the manual. -Type "Make.py -h" for help. Because the mechanism for specifing what -compiler to use (Intel in this case) is different for different MPI -wrappers, 3 versions of the Make.py command are shown. -

    -

    Note that if you build with support for a Phi coprocessor, the same -binary can be used on nodes with or without coprocessors installed. -However, if you do not have coprocessors on your system, building -without offload support will produce a smaller binary. -

    -

    If you also build with the USER-OMP package, you can use styles from -both packages, as described below. -

    -

    Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must -include "-fopenmp". Likewise, if you use an Intel compiler, the -CCFLAGS setting must include "-restrict". For Phi support, the -"-DLMP_INTEL_OFFLOAD" (CCFLAGS) and "-offload" (LINKFLAGS) settings -are required. The other settings listed above are optional, but will -typically improve performance. The Make.py command will add all of -these automatically. -

    -

    If you are compiling on the same architecture that will be used for -the runs, adding the flag -xHost to CCFLAGS enables vectorization -with the Intel(R) compiler. Otherwise, you must provide the correct -compute node architecture to the -x option (e.g. -xAVX). -

    -

    Example machines makefiles Makefile.intel_cpu and Makefile.intel_phi -are included in the src/MAKE/OPTIONS directory with settings that -perform well with the Intel(R) compiler. The latter has support for -offload to Phi coprocessors; the former does not. -

    -

    Run with the USER-INTEL package from the command line: -

    -

    The mpirun or mpiexec command sets the total number of MPI tasks used -by LAMMPS (one or multiple per compute node) and the number of MPI -tasks used per node. E.g. the mpirun command in MPICH does this via -its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. -

    -

    If you compute (any portion of) pairwise interactions using USER-INTEL -pair styles on the CPU, or use USER-OMP styles on the CPU, you need to -choose how many OpenMP threads per MPI task to use. If both packages -are used, it must be done for both packages, and the same thread count -value should be used for both. Note that the product of MPI tasks * -threads/task should not exceed the physical number of cores (on a -node), otherwise performance will suffer. -

    -

    When using the USER-INTEL package for the Phi, you also need to -specify the number of coprocessor/node and optionally the number of -coprocessor threads per MPI task to use. Note that coprocessor -threads (which run on the coprocessor) are totally independent from -OpenMP threads (which run on the CPU). The default values for the -settings that affect coprocessor threads are typically fine, as -discussed below. -

    -

    As in the lines above, use the "-sf intel" or "-sf hybrid intel omp" -command-line switch, which will -automatically append "intel" to styles that support it. In the second -case, "omp" will be appended if an "intel" style does not exist. -

    -

    Note that if either switch is used, it also invokes a default command: -package intel 1. If the "-sf hybrid intel omp" switch -is used, the default USER-OMP command package omp 0 is -also invoked (if LAMMPS was built with USER-OMP). Both set the number -of OpenMP threads per MPI task via the OMP_NUM_THREADS environment -variable. The first command sets the number of Xeon Phi(TM) -coprocessors/node to 1 (ignored if USER-INTEL is built for CPU-only), -and the precision mode to "mixed" (default value). -

    -

    You can also use the "-pk intel Nphi" command-line -switch to explicitly set Nphi = # of Xeon -Phi(TM) coprocessors/node, as well as additional options. Nphi should -be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi -= 0 for a CPU-only build. All the available coprocessor threads on -each Phi will be divided among MPI tasks, unless the tptask option -of the "-pk intel" command-line switch is -used to limit the coprocessor threads per MPI task. See the package -intel command for details, including the default values -used for all its options if not specified, and how to set the number -of OpenMP threads via the OMP_NUM_THREADS environment variable if -desired. -

    -

    If LAMMPS was built with the USER-OMP package, you can also use the -"-pk omp Nt" command-line switch to -explicitly set Nt = # of OpenMP threads per MPI task to use, as well -as additional options. Nt should be the same threads per MPI task as -set for the USER-INTEL package, e.g. via the "-pk intel Nphi omp Nt" -command. Again, see the package omp command for -details, including the default values used for all its options if not -specified, and how to set the number of OpenMP threads via the -OMP_NUM_THREADS environment variable if desired. -

    -

    Or run with the USER-INTEL package by editing an input script: -

    -

    The discussion above for the mpirun/mpiexec command, MPI tasks/node, -OpenMP threads per MPI task, and coprocessor threads per MPI task is -the same. -

    -

    Use the suffix intel or suffix hybrid intel -omp commands, or you can explicitly add an "intel" or -"omp" suffix to individual styles in your input script, e.g. -

    -
    pair_style lj/cut/intel 2.5 
-
    -

    You must also use the package intel command, unless the -"-sf intel" or "-pk intel" command-line -switches were used. It specifies how many -coprocessors/node to use, as well as other OpenMP threading and -coprocessor options. The package doc page explains how -to set the number of OpenMP threads via an environment variable if -desired. -

    -

    If LAMMPS was also built with the USER-OMP package, you must also use -the package omp command to enable that package, unless -the "-sf hybrid intel omp" or "-pk omp" command-line -switches were used. It specifies how many -OpenMP threads per MPI task to use (should be same as the setting for -the USER-INTEL package), as well as other options. Its doc page -explains how to set the number of OpenMP threads via an environment -variable if desired. -

    -

    Speed-ups to expect: -

    -

    If LAMMPS was not built with coprocessor support (CPU only) when -including the USER-INTEL package, then acclerated styles will run on -the CPU using vectorization optimizations and the specified precision. -This may give a substantial speed-up for a pair style, particularly if -mixed or single precision is used. -

    -

    If LAMMPS was built with coproccesor support, the pair styles will run -on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The -performance of a Xeon Phi versus a multi-core CPU is a function of -your hardware, which pair style is used, the number of -atoms/coprocessor, and the precision used on the coprocessor (double, -single, mixed). -

    -

    See the Benchmark page of the -LAMMPS web site for performance of the USER-INTEL package on different -hardware. -

    -

    IMPORTANT NOTE: Setting core affinity is often used to pin MPI tasks -and OpenMP threads to a core or group of cores so that memory access -can be uniform. Unless disabled at build time, affinity for MPI tasks -and OpenMP threads on the host (CPU) will be set by default on the -host when using offload to a coprocessor. In this case, it is -unnecessary to use other methods to control affinity (e.g. taskset, -numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input -script with the no_affinity option to the package -intel command or by disabling the option at build time -(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your -Makefile). Disabling this option is not recommended, especially when -running on a machine with hyperthreading disabled. -

    -

    Guidelines for best performance on an Intel(R) Xeon Phi(TM) -coprocessor: -

    -
    • The default for the package intel command is to have -all the MPI tasks on a given compute node use a single Xeon Phi(TM) -coprocessor. In general, running with a large number of MPI tasks on -each node will perform best with offload. Each MPI task will -automatically get affinity to a subset of the hardware threads -available on the coprocessor. For example, if your card has 61 cores, -with 60 cores available for offload and 4 hardware threads per core -(240 total threads), running with 24 MPI tasks per node will cause -each MPI task to use a subset of 10 threads on the coprocessor. Fine -tuning of the number of threads to use per MPI task or the number of -threads to use per core can be accomplished with keyword settings of -the package intel command. - -
    • If desired, only a fraction of the pair style computation can be -offloaded to the coprocessors. This is accomplished by using the -balance keyword in the package intel command. A -balance of 0 runs all calculations on the CPU. A balance of 1 runs -all calculations on the coprocessor. A balance of 0.5 runs half of -the calculations on the coprocessor. Setting the balance to -1 (the -default) will enable dynamic load balancing that continously adjusts -the fraction of offloaded work throughout the simulation. This option -typically produces results within 5 to 10 percent of the optimal fixed -balance. - -
    • When using offload with CPU hyperthreading disabled, it may help -performance to use fewer MPI tasks and OpenMP threads than available -cores. This is due to the fact that additional threads are generated -internally to handle the asynchronous offload tasks. - -
    • If running short benchmark runs with dynamic load balancing, adding a -short warm-up run (10-20 steps) will allow the load-balancer to find a -near-optimal setting that will carry over to additional runs. - -
    • If pair computations are being offloaded to an Intel(R) Xeon Phi(TM) -coprocessor, a diagnostic line is printed to the screen (not to the -log file), during the setup phase of a run, indicating that offload -mode is being used and indicating the number of coprocessor threads -per MPI task. Additionally, an offload timing summary is printed at -the end of each run. When offloading, the frequency for atom -sorting is changed to 1 so that the per-atom data is -effectively sorted at every rebuild of the neighbor lists. - -
    • For simulations with long-range electrostatics or bond, angle, -dihedral, improper calculations, computation and data transfer to the -coprocessor will run concurrently with computations and MPI -communications for these calculations on the host CPU. The USER-INTEL -package has two modes for deciding which atoms will be handled by the -coprocessor. This choice is controlled with the ghost keyword of -the package intel command. When set to 0, ghost atoms -(atoms at the borders between MPI tasks) are not offloaded to the -card. This allows for overlap of MPI communication of forces with -computation on the coprocessor when the newton setting -is "on". The default is dependent on the style being used, however, -better performance may be achieved by setting this option -explictly. -
    -

    Restrictions: -

    -

    When offloading to a coprocessor, hybrid styles -that require skip lists for neighbor builds cannot be offloaded. -Using hybrid/overlay is allowed. Only one intel -accelerated style may be used with hybrid styles. -Special_bonds exclusion lists are not currently -supported with offload, however, the same effect can often be -accomplished by setting cutoffs for excluded atom types to 0. None of -the pair styles in the USER-INTEL package currently support the -"inner", "middle", "outer" options for rRESPA integration via the -run_style respa command; only the "pair" option is -supported. -

    - diff --git a/doc/doc2/accelerate_kokkos.html b/doc/doc2/accelerate_kokkos.html deleted file mode 100644 index 79240c2bce..0000000000 --- a/doc/doc2/accelerate_kokkos.html +++ /dev/null @@ -1,514 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    Return to Section accelerate overview -

    -

    5.3.4 KOKKOS package -

    -

    The KOKKOS package was developed primarily by Christian Trott (Sandia) -with contributions of various styles by others, including Sikandar -Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia). The -underlying Kokkos library was written primarily by Carter Edwards, -Christian Trott, and Dan Sunderland (all Sandia). -

    -

    The KOKKOS package contains versions of pair, fix, and atom styles -that use data structures and macros provided by the Kokkos library, -which is included with LAMMPS in lib/kokkos. -

    -

    The Kokkos library is part of -Trilinos and can also be -downloaded from Github. Kokkos is a -templated C++ library that provides two key abstractions for an -application like LAMMPS. First, it allows a single implementation of -an application kernel (e.g. a pair style) to run efficiently on -different kinds of hardware, such as a GPU, Intel Phi, or many-core -CPU. -

    -

    The Kokkos library also provides data abstractions to adjust (at -compile time) the memory layout of basic data structures like 2d and -3d arrays and allow the transparent utilization of special hardware -load and store operations. Such data structures are used in LAMMPS to -store atom coordinates or forces or neighbor lists. The layout is -chosen to optimize performance on different platforms. Again this -functionality is hidden from the developer, and does not affect how -the kernel is coded. -

    -

    These abstractions are set at build time, when LAMMPS is compiled with -the KOKKOS package installed. All Kokkos operations occur within the -context of an individual MPI task running on a single node of the -machine. The total number of MPI tasks used by LAMMPS (one or -multiple per compute node) is set in the usual manner via the mpirun -or mpiexec commands, and is independent of Kokkos. -

    -

    Kokkos currently provides support for 3 modes of execution (per MPI -task). These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs), -and OpenMP (for Intel Phi). Note that the KOKKOS package supports -running on the Phi in native mode, not offload mode like the -USER-INTEL package supports. You choose the mode at build time to -produce an executable compatible with specific hardware. -

    -

    Here is a quick overview of how to use the KOKKOS package -for CPU acceleration, assuming one or more 16-core nodes. -More details follow. -

    -

    use a C++11 compatible compiler -make yes-kokkos -make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package -make kokkos_omp # or Makefile.kokkos_omp already has variable set -Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py -

    -
    mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
-mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
-mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task 
-mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks/node, 4 threads/task 
-
    -
    • specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support -
    • include the KOKKOS package and build LAMMPS -
    • enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script -
    -

    Here is a quick overview of how to use the KOKKOS package for GPUs, -assuming one or more nodes, each with 16 cores and a GPU. More -details follow. -

    -

    discuss use of NVCC, which Makefiles to examine -

    -

    use a C++11 compatible compiler -KOKKOS_DEVICES = Cuda, OpenMP -KOKKOS_ARCH = Kepler35 -make yes-kokkos -make machine -Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda -

    -
    mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
-mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes 
-
    -
    mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes 
-
    -

    Here is a quick overview of how to use the KOKKOS package -for the Intel Phi: -

    -
    use a C++11 compatible compiler
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNC
-make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi 
-
    -

    host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading): -mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240 -mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240 -mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240 -mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis -

    -

    Required hardware/software: -

    -

    Kokkos support within LAMMPS must be built with a C++11 compatible -compiler. If using gcc, version 4.8.1 or later is required. -

    -

    To build with Kokkos support for CPUs, your compiler must support the -OpenMP interface. You should have one or more multi-core CPUs so that -multiple threads can be launched by each MPI task running on a CPU. -

    -

    To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software -version 6.5 or later must be installed on your system. See the -discussion for the USER-CUDA and -GPU packages for details of how to check and do -this. -

    -

    IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs, -you must have Kepler generation GPUs (or later). The Kokkos library -exploits texture cache options not supported by Telsa generation GPUs -(or older). -

    -

    To build with Kokkos support for Intel Xeon Phi coprocessors, your -sysmte must be configured to use them in "native" mode, not "offload" -mode like the USER-INTEL package supports. -

    -

    Building LAMMPS with the KOKKOS package: -

    -

    You must choose at build time whether to build for CPUs (OpenMP), -GPUs, or Phi. -

    -

    You can do any of these in one line, using the src/Make.py script, -described in Section 2.4 of the manual. -Type "Make.py -h" for help. If run from the src directory, these -commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and -lmp_kokkos_phi. Note that the OMP and PHI options use -src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA -option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda. -

    -

    The latter two steps can be done using the "-k on", "-pk kokkos" and -"-sf kk" command-line switches -respectively. Or the effect of the "-pk" or "-sf" switches can be -duplicated by adding the package kokkos or suffix -kk commands respectively to your input script. -

    -

    Or you can follow these steps: -

    -

    CPU-only (run all-MPI or with OpenMP threading): -

    -
    cd lammps/src
-make yes-kokkos
-make g++ KOKKOS_DEVICES=OpenMP 
-
    -

    Intel Xeon Phi: -

    -
    cd lammps/src
-make yes-kokkos
-make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC 
-
    -

    CPUs and GPUs: -

    -
    cd lammps/src
-make yes-kokkos
-make cuda KOKKOS_DEVICES=Cuda 
-
    -

    These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the -make command line which requires a GNU-compatible make command. Try -"gmake" if your system's standard make complains. -

    -

    IMPORTANT NOTE: If you build using make line variables and re-build -LAMMPS twice with different KOKKOS options and the *same* target, -e.g. g++ in the first two examples above, then you *must* perform a -"make clean-all" or "make clean-machine" before each build. This is -to force all the KOKKOS-dependent files to be re-compiled with the new -options. -

    -

    You can also hardwire these make variables in the specified machine -makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above, -with a line like: -

    -
    KOKKOS_ARCH = KNC 
-
    -

    Note that if you build LAMMPS multiple times in this manner, using -different KOKKOS options (defined in different machine makefiles), you -do not have to worry about doing a "clean" in between. This is -because the targets will be different. -

    -

    IMPORTANT NOTE: The 3rd example above for a GPU, uses a different -machine makefile, in this case src/MAKE/Makefile.cuda, which is -included in the LAMMPS distribution. To build the KOKKOS package for -a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must -have a KOKKOS_ARCH setting that is appropriate for your NVIDIA -hardware and installed software. Typical values for KOKKOS_ARCH are given -below, as well -as other settings that must be included in the machine makefile, if -you create your own. -

    -

    IMPORTANT NOTE: Currently, there are no precision options with the -KOKKOS package. All compilation and computation is performed in -double precision. -

    -

    There are other allowed options when building with the KOKKOS package. -As above, they can be set either as variables on the make command line -or in Makefile.machine. This is the full list of options, including -those discussed above, Each takes a value shown below. The -default value is listed, which is set in the -lib/kokkos/Makefile.kokkos file. -

    -

    #Default settings specific options -#Options: force_uvm,use_ldg,rdc -

    -
    • KOKKOS_DEVICES, values = OpenMP, Serial, Pthreads, Cuda, default = OpenMP -
    • KOKKOS_ARCH, values = KNC, SNB, HSW, Kepler, Kepler30, Kepler32, Kepler35, Kepler37, Maxwell, Maxwell50, Maxwell52, Maxwell53, ARMv8, BGQ, Power7, Power8, default = none -
    • KOKKOS_DEBUG, values = yes, no, default = no -
    • KOKKOS_USE_TPLS, values = hwloc, librt, default = none -
    • KOKKOS_CUDA_OPTIONS, values = force_uvm, use_ldg, rdc -
    -

    KOKKOS_DEVICE sets the parallelization method used for Kokkos code -(within LAMMPS). KOKKOS_DEVICES=OpenMP means that OpenMP will be -used. KOKKOS_DEVICES=Pthreads means that pthreads will be used. -KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used. -

    -

    If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE -directory must use "nvcc" as its compiler, via its CC setting. For -best performance its CCFLAGS setting should use -O3 and have a -KOKKOS_ARCH setting that matches the compute capability of your NVIDIA -hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note -the minimal required compute capability is 2.0, but this will give -signicantly reduced performance compared to Kepler generation GPUs -with compute capability 3.x. For the LINK setting, "nvcc" should not -be used; instead use g++ or another compiler suitable for linking C++ -applications. Often you will want to use your MPI compiler wrapper -for this setting (i.e. mpicxx). Finally, the lo-level Makefile must -also have a "Compilation rule" for creating *.o files from *.cu files. -See src/Makefile.cuda for an example of a lo-level Makefile with all -of these settings. -

    -

    KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not -migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be -used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not -necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP -provides alternative methods via environment variables for binding -threads to hardware cores. More info on binding threads to cores is -given in this section. -

    -

    KOKKOS_ARCH=KNC enables compiler switches needed when compling for an -Intel Phi processor. -

    -

    KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism -on most Unix platforms. This library is not available on all -platforms. -

    -

    KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style -within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time -debugging information that can be useful. It also enables runtime -bounds checking on Kokkos data structures. -

    -

    KOKKOS_CUDA_OPTIONS are additional options for CUDA. -

    -

    For more information on Kokkos see the Kokkos programmers' guide here: -/lib/kokkos/doc/Kokkos_PG.pdf. -

    -

    Run with the KOKKOS package from the command line: -

    -

    The mpirun or mpiexec command sets the total number of MPI tasks used -by LAMMPS (one or multiple per compute node) and the number of MPI -tasks used per node. E.g. the mpirun command in MPICH does this via -its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. -

    -

    When using KOKKOS built with host=OMP, you need to choose how many -OpenMP threads per MPI task will be used (via the "-k" command-line -switch discussed below). Note that the product of MPI tasks * OpenMP -threads/task should not exceed the physical number of cores (on a -node), otherwise performance will suffer. -

    -

    When using the KOKKOS package built with device=CUDA, you must use -exactly one MPI task per physical GPU. -

    -

    When using the KOKKOS package built with host=MIC for Intel Xeon Phi -coprocessor support you need to insure there are one or more MPI tasks -per coprocessor, and choose the number of coprocessor threads to use -per MPI task (via the "-k" command-line switch discussed below). The -product of MPI tasks * coprocessor threads/task should not exceed the -maximum number of threads the coproprocessor is designed to run, -otherwise performance will suffer. This value is 240 for current -generation Xeon Phi(TM) chips, which is 60 physical cores * 4 -threads/core. Note that with the KOKKOS package you do not need to -specify how many Phi coprocessors there are per node; each -coprocessors is simply treated as running some number of MPI tasks. -

    -

    You must use the "-k on" command-line -switch to enable the KOKKOS package. It -takes additional arguments for hardware settings appropriate to your -system. Those arguments are documented -here. The two most commonly used -options are: -

    -
    -k on t Nt g Ng 
-
    -

    The "t Nt" option applies to host=OMP (even if device=CUDA) and -host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI -task to use with a node. For host=MIC, it specifies how many Xeon Phi -threads per MPI task to use within a node. The default is Nt = 1. -Note that for host=OMP this is effectively MPI-only mode which may be -fine. But for host=MIC you will typically end up using far less than -all the 240 available threads, which could give very poor performance. -

    -

    The "g Ng" option applies to device=CUDA. It specifies how many GPUs -per compute node to use. The default is 1, so this only needs to be -specified is you have 2 or more GPUs per compute node. -

    -

    The "-k on" switch also issues a "package kokkos" command (with no -additional arguments) which sets various KOKKOS options to default -values, as discussed on the package command doc page. -

    -

    Use the "-sf kk" command-line switch, -which will automatically append "kk" to styles that support it. Use -the "-pk kokkos" command-line switch if -you wish to change any of the default package kokkos -optionns set by the "-k on" command-line -switch. -

    -

    Note that the default for the package kokkos command is -to use "full" neighbor lists and set the Newton flag to "off" for both -pairwise and bonded interactions. This typically gives fastest -performance. If the newton command is used in the input -script, it can override the Newton flag defaults. -

    -

    However, when running in MPI-only mode with 1 thread per MPI task, it -will typically be faster to use "half" neighbor lists and set the -Newton flag to "on", just as is the case for non-accelerated pair -styles. You can do this with the "-pk" command-line -switch. -

    -

    Or run with the KOKKOS package by editing an input script: -

    -

    The discussion above for the mpirun/mpiexec command and setting -appropriate thread and GPU values for host=OMP or host=MIC or -device=CUDA are the same. -

    -

    You must still use the "-k on" command-line -switch to enable the KOKKOS package, and -specify its additional arguments for hardware options appopriate to -your system, as documented above. -

    -

    Use the suffix kk command, or you can explicitly add a -"kk" suffix to individual styles in your input script, e.g. -

    -
    pair_style lj/cut/kk 2.5 
-
    -

    You only need to use the package kokkos command if you -wish to change any of its option defaults, as set by the "-k on" -command-line switch. -

    -

    Speed-ups to expect: -

    -

    The performance of KOKKOS running in different modes is a function of -your hardware, which KOKKOS-enable styles are used, and the problem -size. -

    -

    Generally speaking, the following rules of thumb apply: -

    -
    • When running on CPUs only, with a single thread per MPI task, -performance of a KOKKOS style is somewhere between the standard -(un-accelerated) styles (MPI-only mode), and those provided by the -USER-OMP package. However the difference between all 3 is small (less -than 20%). - -
    • When running on CPUs only, with multiple threads per MPI task, -performance of a KOKKOS style is a bit slower than the USER-OMP -package. - -
    • When running on GPUs, KOKKOS is typically faster than the USER-CUDA -and GPU packages. - -
    • When running on Intel Xeon Phi, KOKKOS is not as fast as -the USER-INTEL package, which is optimized for that hardware. -
    -

    See the Benchmark page of the -LAMMPS web site for performance of the KOKKOS package on different -hardware. -

    -

    Guidelines for best performance: -

    -

    Here are guidline for using the KOKKOS package on the different -hardware configurations listed above. -

    -

    Many of the guidelines use the package kokkos command -See its doc page for details and default settings. Experimenting with -its options can provide a speed-up for specific calculations. -

    -

    Running on a multi-core CPU: -

    -

    If N is the number of physical cores/node, then the number of MPI -tasks/node * number of threads/task should not exceed N, and should -typically equal N. Note that the default threads/task is 1, as set by -the "t" keyword of the "-k" command-line -switch. If you do not change this, no -additional parallelism (beyond MPI) will be invoked on the host -CPU(s). -

    -

    You can compare the performance running in different modes: -

    -
    • run with 1 MPI task/node and N threads/task -
    • run with N MPI tasks/node and 1 thread/task -
    • run with settings in between these extremes -
    -

    Examples of mpirun commands in these modes are shown above. -

    -

    When using KOKKOS to perform multi-threading, it is important for -performance to bind both MPI tasks to physical cores, and threads to -physical cores, so they do not migrate during a simulation. -

    -

    If you are not certain MPI tasks are being bound (check the defaults -for your MPI installation), binding can be forced with these flags: -

    -
    OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
-Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ... 
-
    -

    For binding threads with the KOKKOS OMP option, use thread affinity -environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or -later, intel 12 or later) setting the environment variable -OMP_PROC_BIND=true should be sufficient. For binding threads with the -KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as -discussed in Section 2.3.4 of the -manual. -

    -

    Running on GPUs: -

    -

    Insure the -arch setting in the machine makefile you are using, -e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software -(see this section of the manual for -details). -

    -

    The -np setting of the mpirun command should set the number of MPI -tasks/node to be equal to the # of physical GPUs on the node. -

    -

    Use the "-k" command-line switch to -specify the number of GPUs per node, and the number of threads per MPI -task. As above for multi-core CPUs (and no GPU), if N is the number -of physical cores/node, then the number of MPI tasks/node * number of -threads/task should not exceed N. With one GPU (and one MPI task) it -may be faster to use less than all the available cores, by setting -threads/task to a smaller value. This is because using all the cores -on a dual-socket node will incur extra cost to copy memory from the -2nd socket to the GPU. -

    -

    Examples of mpirun commands that follow these rules are shown above. -

    -

    IMPORTANT NOTE: When using a GPU, you will achieve the best -performance if your input script does not use any fix or compute -styles which are not yet Kokkos-enabled. This allows data to stay on -the GPU for multiple timesteps, without being copied back to the host -CPU. Invoking a non-Kokkos fix or compute, or performing I/O for -thermo or dump output will cause data -to be copied back to the CPU. -

    -

    You cannot yet assign multiple MPI tasks to the same GPU with the -KOKKOS package. We plan to support this in the future, similar to the -GPU package in LAMMPS. -

    -

    You cannot yet use both the host (multi-threaded) and device (GPU) -together to compute pairwise interactions with the KOKKOS package. We -hope to support this in the future, similar to the GPU package in -LAMMPS. -

    -

    Running on an Intel Phi: -

    -

    Kokkos only uses Intel Phi processors in their "native" mode, i.e. -not hosted by a CPU. -

    -

    As illustrated above, build LAMMPS with OMP=yes (the default) and -MIC=yes. The latter insures code is correctly compiled for the Intel -Phi. The OMP setting means OpenMP will be used for parallelization on -the Phi, which is currently the best option within Kokkos. In the -future, other options may be added. -

    -

    Current-generation Intel Phi chips have either 61 or 57 cores. One -core should be excluded for running the OS, leaving 60 or 56 cores. -Each core is hyperthreaded, so there are effectively N = 240 (4*60) or -N = 224 (4*56) cores to run on. -

    -

    The -np setting of the mpirun command sets the number of MPI -tasks/node. The "-k on t Nt" command-line switch sets the number of -threads/task as Nt. The product of these 2 values should be N, i.e. -240 or 224. Also, the number of threads/task should be a multiple of -4 so that logical threads from more than one MPI task do not run on -the same physical core. -

    -

    Examples of mpirun commands that follow these rules are shown above. -

    -

    Restrictions: -

    -

    As noted above, if using GPUs, the number of MPI tasks per compute -node should equal to the number of GPUs per compute node. In the -future Kokkos will support assigning multiple MPI tasks to a single -GPU. -

    -

    Currently Kokkos does not support AMD GPUs due to limits in the -available backend programming models. Specifically, Kokkos requires -extensive C++ support from the Kernel language. This is expected to -change in the future. -

    - diff --git a/doc/doc2/accelerate_omp.html b/doc/doc2/accelerate_omp.html deleted file mode 100644 index c898c3d11d..0000000000 --- a/doc/doc2/accelerate_omp.html +++ /dev/null @@ -1,191 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    Return to Section accelerate overview -

    -

    5.3.5 USER-OMP package -

    -

    The USER-OMP package was developed by Axel Kohlmeyer at Temple -University. It provides multi-threaded versions of most pair styles, -nearly all bonded styles (bond, angle, dihedral, improper), several -Kspace styles, and a few fix styles. The package currently uses the -OpenMP interface for multi-threading. -

    -

    Here is a quick overview of how to use the USER-OMP package, assuming -one or more 16-core nodes. More details follow. -

    -
    use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
-make yes-user-omp
-make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi
-make omp                                   # or Makefile.omp already has settings
-Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py 
-
    -
    lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
-mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
-mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task 
-
    -

    Required hardware/software: -

    -

    Your compiler must support the OpenMP interface. You should have one -or more multi-core CPUs so that multiple threads can be launched by -each MPI task running on a CPU. -

    -

    Building LAMMPS with the USER-OMP package: -

    -

    The lines above illustrate how to include/build with the USER-OMP -package in two steps, using the "make" command. Or how to do it with -one command via the src/Make.py script, described in Section -2.4 of the manual. Type "Make.py -h" for -help. -

    -

    Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must -include "-fopenmp". Likewise, if you use an Intel compiler, the -CCFLAGS setting must include "-restrict". The Make.py command will -add these automatically. -

    -

    Run with the USER-OMP package from the command line: -

    -

    The mpirun or mpiexec command sets the total number of MPI tasks used -by LAMMPS (one or multiple per compute node) and the number of MPI -tasks used per node. E.g. the mpirun command in MPICH does this via -its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. -

    -

    You need to choose how many OpenMP threads per MPI task will be used -by the USER-OMP package. Note that the product of MPI tasks * -threads/task should not exceed the physical number of cores (on a -node), otherwise performance will suffer. -

    -

    As in the lines above, use the "-sf omp" command-line -switch, which will automatically append -"omp" to styles that support it. The "-sf omp" switch also issues a -default package omp 0 command, which will set the -number of threads per MPI task via the OMP_NUM_THREADS environment -variable. -

    -

    You can also use the "-pk omp Nt" command-line -switch, to explicitly set Nt = # of OpenMP -threads per MPI task to use, as well as additional options. Its -syntax is the same as the package omp command whose doc -page gives details, including the default values used if it is not -specified. It also gives more details on how to set the number of -threads via the OMP_NUM_THREADS environment variable. -

    -

    Or run with the USER-OMP package by editing an input script: -

    -

    The discussion above for the mpirun/mpiexec command, MPI tasks/node, -and threads/MPI task is the same. -

    -

    Use the suffix omp command, or you can explicitly add an -"omp" suffix to individual styles in your input script, e.g. -

    -
    pair_style lj/cut/omp 2.5 
-
    -

    You must also use the package omp command to enable the -USER-OMP package. When you do this you also specify how many threads -per MPI task to use. The command doc page explains other options and -how to set the number of threads via the OMP_NUM_THREADS environment -variable. -

    -

    Speed-ups to expect: -

    -

    Depending on which styles are accelerated, you should look for a -reduction in the "Pair time", "Bond time", "KSpace time", and "Loop -time" values printed at the end of a run. -

    -

    You may see a small performance advantage (5 to 20%) when running a -USER-OMP style (in serial or parallel) with a single thread per MPI -task, versus running standard LAMMPS with its standard un-accelerated -styles (in serial or all-MPI parallelization with 1 task/core). This -is because many of the USER-OMP styles contain similar optimizations -to those used in the OPT package, described in Section accelerate -5.3.6. -

    -

    With multiple threads/task, the optimal choice of number of MPI -tasks/node and OpenMP threads/task can vary a lot and should always be -tested via benchmark runs for a specific simulation running on a -specific machine, paying attention to guidelines discussed in the next -sub-section. -

    -

    A description of the multi-threading strategy used in the USER-OMP -package and some performance examples are presented -here -

    -

    Guidelines for best performance: -

    -

    For many problems on current generation CPUs, running the USER-OMP -package with a single thread/task is faster than running with multiple -threads/task. This is because the MPI parallelization in LAMMPS is -often more efficient than multi-threading as implemented in the -USER-OMP package. The parallel efficiency (in a threaded sense) also -varies for different USER-OMP styles. -

    -

    Using multiple threads/task can be more effective under the following -circumstances: -

    -
    • Individual compute nodes have a significant number of CPU cores but -the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx -(Clovertown) and 54xx (Harpertown) quad-core processors. Running one -MPI task per CPU core will result in significant performance -degradation, so that running with 4 or even only 2 MPI tasks per node -is faster. Running in hybrid MPI+OpenMP mode will reduce the -inter-node communication bandwidth contention in the same way, but -offers an additional speedup by utilizing the otherwise idle CPU -cores. - -
    • The interconnect used for MPI communication does not provide -sufficient bandwidth for a large number of MPI tasks per node. For -example, this applies to running over gigabit ethernet or on Cray XT4 -or XT5 series supercomputers. As in the aforementioned case, this -effect worsens when using an increasing number of nodes. - -
    • The system has a spatially inhomogeneous particle density which does -not map well to the domain decomposition scheme or -load-balancing options that LAMMPS provides. This is -because multi-threading achives parallelism over the number of -particles, not via their distribution in space. - -
    • A machine is being used in "capability mode", i.e. near the point -where MPI parallelism is maxed out. For example, this can happen when -using the PPPM solver for long-range -electrostatics on large numbers of nodes. The scaling of the KSpace -calculation (see the kspace_style command) becomes -the performance-limiting factor. Using multi-threading allows less -MPI tasks to be invoked and can speed-up the long-range solver, while -increasing overall performance by parallelizing the pairwise and -bonded calculations via OpenMP. Likewise additional speedup can be -sometimes be achived by increasing the length of the Coulombic cutoff -and thus reducing the work done by the long-range solver. Using the -run_style verlet/split command, which is compatible -with the USER-OMP package, is an alternative way to reduce the number -of MPI tasks assigned to the KSpace calculation. -
    -

    Additional performance tips are as follows: -

    -
    • The best parallel efficiency from omp styles is typically achieved -when there is at least one MPI task per physical CPU chip, i.e. socket -or die. - -
    • It is usually most efficient to restrict threading to a single -socket, i.e. use one or more MPI task per socket. - -
    • IMPORTANT NOTE: By default, several current MPI implementations use a -processor affinity setting that restricts each MPI task to a single -CPU core. Using multi-threading in this mode will force all threads -to share the one core and thus is likely to be counterproductive. -Instead, binding MPI tasks to a (multi-core) socket, should solve this -issue. -
    -

    Restrictions: -

    -

    None. -

    - diff --git a/doc/doc2/accelerate_opt.html b/doc/doc2/accelerate_opt.html deleted file mode 100644 index 53613ba2bd..0000000000 --- a/doc/doc2/accelerate_opt.html +++ /dev/null @@ -1,76 +0,0 @@ - -
    Previous Section - LAMMPS WWW Site - -LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    Return to Section accelerate overview -

    -

    5.3.6 OPT package -

    -

    The OPT package was developed by James Fischer (High Performance -Technologies), David Richie, and Vincent Natoli (Stone Ridge -Technologies). It contains a handful of pair styles whose compute() -methods were rewritten in C++ templated form to reduce the overhead -due to if tests and other conditional code. -

    -

    Here is a quick overview of how to use the OPT package. More details -follow. -

    -
    make yes-opt
-make mpi                               # build with the OPT pacakge
-Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py 
-
    -
    lmp_mpi -sf opt -in in.script                # run in serial
-mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel 
-
    -

    Required hardware/software: -

    -

    None. -

    -

    Building LAMMPS with the OPT package: -

    -

    The lines above illustrate how to build LAMMPS with the OPT package in -two steps, using the "make" command. Or how to do it with one command -via the src/Make.py script, described in Section -2.4 of the manual. Type "Make.py -h" for -help. -

    -

    Note that if you use an Intel compiler to build with the OPT package, -the CCFLAGS setting in your Makefile.machine must include "-restrict". -The Make.py command will add this automatically. -

    -

    Run with the OPT package from the command line: -

    -

    As in the lines above, use the "-sf opt" command-line -switch, which will automatically append -"opt" to styles that support it. -

    -

    Or run with the OPT package by editing an input script: -

    -

    Use the suffix opt command, or you can explicitly add an -"opt" suffix to individual styles in your input script, e.g. -

    -
    pair_style lj/cut/opt 2.5 
-
    -

    Speed-ups to expect: -

    -

    You should see a reduction in the "Pair time" value printed at the end -of a run. On most machines for reasonable problem sizes, it will be a -5 to 20% savings. -

    -

    Guidelines for best performance: -

    -

    Just try out an OPT pair style to see how it performs. -

    -

    Restrictions: -

    -

    None. -

    - diff --git a/doc/doc2/angle_charmm.html b/doc/doc2/angle_charmm.html deleted file mode 100644 index bfac8e0760..0000000000 --- a/doc/doc2/angle_charmm.html +++ /dev/null @@ -1,97 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style charmm command -

    -

    angle_style charmm/kk command -

    -

    angle_style charmm/omp command -

    -

    Syntax: -

    -
    angle_style charmm 
-
    -

    Examples: -

    -
    angle_style charmm
-angle_coeff 1 300.0 107.0 50.0 3.0 
-
    -

    Description: -

    -

    The charmm angle style uses the potential -

    -
    -
    -

    with an additional Urey_Bradley term based on the distance r between -the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are -coefficients defined for each angle type. -

    -

    See (MacKerell) for a description of the CHARMM force -field. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy/radian^2) -
    • theta0 (degrees) -
    • K_ub (energy/distance^2) -
    • r_ub (distance) -
    -

    Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    -
    - - - -

    (MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). -

    - diff --git a/doc/doc2/angle_class2.html b/doc/doc2/angle_class2.html deleted file mode 100644 index df2f305a9b..0000000000 --- a/doc/doc2/angle_class2.html +++ /dev/null @@ -1,126 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style class2 command -

    -

    angle_style class2/omp command -

    -

    Syntax: -

    -
    angle_style class2 
-
    -

    Examples: -

    -
    angle_style class2
-angle_coeff * 75.0
-angle_coeff 1 bb 10.5872 1.0119 1.5228
-angle_coeff * ba 3.6551 24.895 1.0119 1.5228 
-
    -

    Description: -

    -

    The class2 angle style uses the potential -

    -
    -
    -

    where Ea is the angle term, Ebb is a bond-bond term, and Eba is a -bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are -the equilibrium bond lengths. -

    -

    See (Sun) for a description of the COMPASS class2 force field. -

    -

    Coefficients for the Ea, Ebb, and Eba formulas must be defined for -each angle type via the angle_coeff command as in -the example above, or in the data file or restart files read by the -read_data or read_restart -commands. -

    -

    These are the 4 coefficients for the Ea formula: -

    -
    • theta0 (degrees) -
    • K2 (energy/radian^2) -
    • K3 (energy/radian^3) -
    • K4 (energy/radian^4) -
    -

    Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of the various K are in per-radian. -

    -

    For the Ebb formula, each line in a angle_coeff -command in the input script lists 4 coefficients, the first of which -is "bb" to indicate they are BondBond coefficients. In a data file, -these coefficients should be listed under a "BondBond Coeffs" heading -and you must leave out the "bb", i.e. only list 3 coefficients after -the angle type. -

    -
    • bb -
    • M (energy/distance^2) -
    • r1 (distance) -
    • r2 (distance) -
    -

    For the Eba formula, each line in a angle_coeff -command in the input script lists 5 coefficients, the first of which -is "ba" to indicate they are BondAngle coefficients. In a data file, -these coefficients should be listed under a "BondAngle Coeffs" heading -and you must leave out the "ba", i.e. only list 4 coefficients after -the angle type. -

    -
    • ba -
    • N1 (energy/distance^2) -
    • N2 (energy/distance^2) -
    • r1 (distance) -
    • r2 (distance) -
    -

    The theta0 value in the Eba formula is not specified, since it is the -same value from the Ea formula. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the CLASS2 -package. See the Making LAMMPS section -for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    -
    - - - -

    (Sun) Sun, J Phys Chem B 102, 7338-7364 (1998). -

    - diff --git a/doc/doc2/angle_coeff.html b/doc/doc2/angle_coeff.html deleted file mode 100644 index 1ae29b5f2c..0000000000 --- a/doc/doc2/angle_coeff.html +++ /dev/null @@ -1,104 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_coeff command -

    -

    Syntax: -

    -
    angle_coeff N args 
-
    -
    • N = angle type (see asterisk form below) -
    • args = coefficients for one or more angle types -
    -

    Examples: -

    -
    angle_coeff 1 300.0 107.0
-angle_coeff * 5.0
-angle_coeff 2*10 5.0 
-
    -

    Description: -

    -

    Specify the angle force field coefficients for one or more angle types. -The number and meaning of the coefficients depends on the angle style. -Angle coefficients can also be set in the data file read by the -read_data command or in a restart file. -

    -

    N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple angle types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). -

    -

    Note that using an angle_coeff command can override a previous setting -for the same angle type. For example, these commands set the coeffs -for all angle types, then overwrite the coeffs for just angle type 2: -

    -
    angle_coeff * 200.0 107.0 1.2
-angle_coeff 2 50.0 107.0 
-
    -

    A line in a data file that specifies angle coefficients uses the exact -same format as the arguments of the angle_coeff command in an input -script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Angle Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as -

    -
    1 300.0 107.0 
-
    -

    The angle_style class2 is an exception to this -rule, in that an additional argument is used in the input script to -allow specification of the cross-term coefficients. See its -doc page for details. -

    -
    - -

    Here is an alphabetic list of angle styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated angle_coeff command. -

    -

    Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of this -page. -

    - - -
    - -

    Restrictions: -

    -

    This command must come after the simulation box is defined by a -read_data, read_restart, or -create_box command. -

    -

    An angle style must be defined before any angle coefficients are -set, either in the input script or in a data file. -

    -

    Related commands: -

    -

    angle_style -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_cosine.html b/doc/doc2/angle_cosine.html deleted file mode 100644 index 709444b5ad..0000000000 --- a/doc/doc2/angle_cosine.html +++ /dev/null @@ -1,77 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style cosine command -

    -

    angle_style cosine/omp command -

    -

    Syntax: -

    -
    angle_style cosine 
-
    -

    Examples: -

    -
    angle_style cosine
-angle_coeff * 75.0 
-
    -

    Description: -

    -

    The cosine angle style uses the potential -

    -
    -
    -

    where K is defined for each angle type. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_cosine_delta.html b/doc/doc2/angle_cosine_delta.html deleted file mode 100644 index e7ce77ead4..0000000000 --- a/doc/doc2/angle_cosine_delta.html +++ /dev/null @@ -1,83 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style cosine/delta command -

    -

    angle_style cosine/delta/omp command -

    -

    Syntax: -

    -
    angle_style cosine/delta 
-
    -

    Examples: -

    -
    angle_style cosine/delta
-angle_coeff 2*4 75.0 100.0 
-
    -

    Description: -

    -

    The cosine/delta angle style uses the potential -

    -
    -
    -

    where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    • theta0 (degrees) -
    -

    Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff, angle_style -cosine/squared -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_cosine_periodic.html b/doc/doc2/angle_cosine_periodic.html deleted file mode 100644 index 58878bb6aa..0000000000 --- a/doc/doc2/angle_cosine_periodic.html +++ /dev/null @@ -1,97 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style cosine/periodic command -

    -

    angle_style cosine/periodic/omp command -

    -

    Syntax: -

    -
    angle_style cosine/periodic 
-
    -

    Examples: -

    -
    angle_style cosine/periodic
-angle_coeff * 75.0 1 6 
-
    -

    Description: -

    -

    The cosine/periodic angle style uses the following potential, which -is commonly used in the DREIDING force -field, particularly for organometallic systems where n = 4 might be -used for an octahedral complex and n = 3 might be used for a -trigonal center: -

    -
    -
    -

    where C, B and n are coefficients defined for each angle type. -

    -

    See (Mayo) for a description of the DREIDING force field -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • C (energy) -
    • B = 1 or -1 -
    • n = 1, 2, 3, 4, 5 or 6 for periodicity -
    -

    Note that the prefactor C is specified and not the overall force -constant K = C / n^2. When B = 1, it leads to a minimum for the -linear geometry. When B = -1, it leads to a maximum for the linear -geometry. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    -
    - - - -

    (Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). -

    - diff --git a/doc/doc2/angle_cosine_shift.html b/doc/doc2/angle_cosine_shift.html deleted file mode 100644 index a7ecc30ae3..0000000000 --- a/doc/doc2/angle_cosine_shift.html +++ /dev/null @@ -1,81 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style cosine/shift command -

    -

    angle_style cosine/shift/omp command -

    -

    Syntax: -

    -
    angle_style cosine/shift 
-
    -

    Examples: -

    -
    angle_style cosine/shift
-angle_coeff * 10.0 45.0 
-
    -

    Description: -

    -

    The cosine/shift angle style uses the potential -

    -
    -
    -

    where theta0 is the equilibrium angle. The potential is bounded -between -Umin and zero. In the neighborhood of the minimum E=- Umin + -Umin/4(theta-theta0)^2 hence the spring constant is umin/2. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • umin (energy) -
    • theta (angle) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff, -angle_cosineshiftexp -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_cosine_shift_exp.html b/doc/doc2/angle_cosine_shift_exp.html deleted file mode 100644 index 14b9e71ede..0000000000 --- a/doc/doc2/angle_cosine_shift_exp.html +++ /dev/null @@ -1,94 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style cosine/shift/exp command -

    -

    angle_style cosine/shift/exp/omp command -

    -

    Syntax: -

    -
    angle_style cosine/shift/exp 
-
    -

    Examples: -

    -
    angle_style cosine/shift/exp
-angle_coeff * 10.0 45.0 2.0 
-
    -

    Description: -

    -

    The cosine/shift/exp angle style uses the potential -

    -
    -
    -

    where Umin, theta, and a are defined for each angle type. -

    -

    The potential is bounded between [-Umin:0] and the minimum is -located at the angle theta0. The a parameter can be both positive or -negative and is used to control the spring constant at the -equilibrium. -

    -

    The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)]. -For a > 3, k/Umin = a/2 to better than 5% relative error. For negative -values of the a parameter, the spring constant is essentially zero, -and anharmonic terms takes over. The potential is furthermore well -behaved in the limit a -> 0, where it has been implemented to linear -order in a for a < 0.001. In this limit the potential reduces to the -cosineshifted potential. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • umin (energy) -
    • theta (angle) -
    • A (real number) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff, -angle_cosineshift, -dihedral_cosineshift -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_cosine_squared.html b/doc/doc2/angle_cosine_squared.html deleted file mode 100644 index 7f85d3552b..0000000000 --- a/doc/doc2/angle_cosine_squared.html +++ /dev/null @@ -1,82 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style cosine/squared command -

    -

    angle_style cosine/squared/omp command -

    -

    Syntax: -

    -
    angle_style cosine/squared 
-
    -

    Examples: -

    -
    angle_style cosine/squared
-angle_coeff 2*4 75.0 100.0 
-
    -

    Description: -

    -

    The cosine/squared angle style uses the potential -

    -
    -
    -

    where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    • theta0 (degrees) -
    -

    Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_dipole.html b/doc/doc2/angle_dipole.html deleted file mode 100644 index b9117b3da9..0000000000 --- a/doc/doc2/angle_dipole.html +++ /dev/null @@ -1,130 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style dipole command -

    -

    angle_style dipole/omp command -

    -

    Syntax: -

    -
    angle_style dipole 
-
    -

    Examples: -

    -
    angle_style dipole
-angle_coeff 6 2.1 180.0 
-
    -

    Description: -

    -

    The dipole angle style is used to control the orientation of a dipolar -atom within a molecule (Orsi). Specifically, the dipole angle -style restrains the orientation of a point dipole mu_j (embedded in atom -'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i' -is another atom of the same molecule (typically, 'i' and 'j' are also -covalently bonded). -

    -

    It is convenient to define an angle gamma between the 'free' vector mu_j -and the reference (bond) vector r_ij: -

    -
    -
    -

    The dipole angle style uses the potential: -

    -
    -
    -

    where K is a rigidity constant and gamma0 is an equilibrium (reference) -angle. -

    -

    The torque on the dipole can be obtained by differentiating the -potential using the 'chain rule' as in appendix C.3 of -(Allen): -

    -
    -
    -

    Example: if gamma0 is set to 0 degrees, the torque generated by -the potential will tend to align the dipole along the reference -direction defined by the (bond) vector r_ij (in other words, mu_j is -restrained to point towards atom 'i'). -

    -

    Note that the angle dipole potential does not give rise to any force, -because it does not depend on the distance between i and j (it only -depends on the angle between mu_j and r_ij). -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    • gamma0 (degrees) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    IMPORTANT NOTE: In the "Angles" section of the data file, the atom ID -'j' corresponding to the dipole to restrain must come before the atom -ID of the reference atom 'i'. A third atom ID 'k' must also be -provided, although 'k' is just a 'dummy' atom which can be any atom; -it may be useful to choose a convention (e.g., 'k'='i') and adhere to -it. For example, if ID=1 for the dipolar atom to restrain, and ID=2 -for the reference atom, the corresponding line in the "Angles" section -of the data file would read: X X 1 2 2 -

    -

    The "newton" command for intramolecular interactions must be "on" -(which is the default). -

    -

    This angle style should not be used with SHAKE. -

    -

    Related commands: -

    -

    angle_coeff, angle_hybrid -

    -

    Default: none -

    -
    - - - -

    (Orsi) Orsi & Essex, The ELBA force field for coarse-grain modeling of -lipid membranes, PloS ONE 6(12): e28637, 2011. -

    - - -

    (Allen) Allen & Tildesley, Computer Simulation of Liquids, -Clarendon Press, Oxford, 1987. -

    - diff --git a/doc/doc2/angle_fourier.html b/doc/doc2/angle_fourier.html deleted file mode 100644 index 93d1b083de..0000000000 --- a/doc/doc2/angle_fourier.html +++ /dev/null @@ -1,78 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style fourier command -

    -

    angle_style fourier/omp command -

    -

    Syntax: -

    -
    angle_style fourier 
-
    -

    Examples: -

    -

    angle_style fourier -angle_coeff 75.0 1.0 1.0 1.0 -

    -

    Description: -

    -

    The fourier angle style uses the potential -

    -
    -
    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    • C0 (real) -
    • C1 (real) -
    • C2 (real) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_fourier_simple.html b/doc/doc2/angle_fourier_simple.html deleted file mode 100644 index 732ee095cc..0000000000 --- a/doc/doc2/angle_fourier_simple.html +++ /dev/null @@ -1,77 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style fourier/simple command -

    -

    angle_style fourier/simple/omp command -

    -

    Syntax: -

    -
    angle_style fourier/simple 
-
    -

    Examples: -

    -

    angle_style fourier/simple -angle_coeff 100.0 -1.0 1.0 -

    -

    Description: -

    -

    The fourier/simple angle style uses the potential -

    -
    -
    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    • c (real) -
    • n (real) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_harmonic.html b/doc/doc2/angle_harmonic.html deleted file mode 100644 index f5b02202ef..0000000000 --- a/doc/doc2/angle_harmonic.html +++ /dev/null @@ -1,84 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style harmonic command -

    -

    angle_style harmonic/kk command -

    -

    angle_style harmonic/omp command -

    -

    Syntax: -

    -
    angle_style harmonic 
-
    -

    Examples: -

    -
    angle_style harmonic
-angle_coeff 1 300.0 107.0 
-
    -

    Description: -

    -

    The harmonic angle style uses the potential -

    -
    -
    -

    where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy/radian^2) -
    • theta0 (degrees) -
    -

    Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: none -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_hybrid.html b/doc/doc2/angle_hybrid.html deleted file mode 100644 index d5e3412fbb..0000000000 --- a/doc/doc2/angle_hybrid.html +++ /dev/null @@ -1,96 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style hybrid command -

    -

    Syntax: -

    -
    angle_style hybrid style1 style2 ... 
-
    -
    • style1,style2 = list of one or more angle styles -
    -

    Examples: -

    -
    angle_style hybrid harmonic cosine
-angle_coeff 1 harmonic 80.0 30.0
-angle_coeff 2* cosine 50.0  
-
    -

    Description: -

    -

    The hybrid style enables the use of multiple angle styles in one -simulation. An angle style is assigned to each angle type. For -example, angles in a polymer flow (of angle type 1) could be computed -with a harmonic potential and angles in the wall boundary (of angle -type 2) could be computed with a cosine potential. The assignment -of angle type to style is made via the angle_coeff -command or in the data file. -

    -

    In the angle_coeff commands, the name of an angle style must be added -after the angle type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 angle_coeff -commands set angles of angle type 1 to be computed with a harmonic -potential with coefficients 80.0, 30.0 for K, theta0. All other angle -types (2-N) are computed with a cosine potential with coefficient -50.0 for K. -

    -

    If angle coefficients are specified in the data file read via the -read_data command, then the same rule applies. -E.g. "harmonic" or "cosine", must be added after the angle type, for each -line in the "Angle Coeffs" section, e.g. -

    -
    Angle Coeffs 
-
    -
    1 harmonic 80.0 30.0
-2 cosine 50.0
-... 
-
    -

    If class2 is one of the angle hybrid styles, the same rule holds for -specifying additional BondBond (and BondAngle) coefficients either via -the input script or in the data file. I.e. class2 must be added to -each line after the angle type. For lines in the BondBond (or -BondAngle) section of the data file for angle types that are not -class2, you must use an angle style of skip as a placeholder, e.g. -

    -
    BondBond Coeffs 
-
    -
    1 skip
-2 class2 3.6512 1.0119 1.0119
-... 
-
    -

    Note that it is not necessary to use the angle style skip in the -input script, since BondBond (or BondAngle) coefficients need not be -specified at all for angle types that are not class2. -

    -

    An angle style of none with no additional coefficients can be used -in place of an angle style, either in a input script angle_coeff -command or in the data file, if you desire to turn off interactions -for specific angle types. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Unlike other angle styles, the hybrid angle style does not store angle -coefficient info for individual sub-styles in a binary restart -files. Thus when retarting a simulation from a restart -file, you need to re-specify angle_coeff commands. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_none.html b/doc/doc2/angle_none.html deleted file mode 100644 index a589bcc7c2..0000000000 --- a/doc/doc2/angle_none.html +++ /dev/null @@ -1,34 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style none command -

    -

    Syntax: -

    -
    angle_style none 
-
    -

    Examples: -

    -
    angle_style none 
-
    -

    Description: -

    -

    Using an angle style of none means angle forces are not computed, even -if triplets of angle atoms were listed in the data file read by the -read_data command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_quartic.html b/doc/doc2/angle_quartic.html deleted file mode 100644 index 9618b3d7f8..0000000000 --- a/doc/doc2/angle_quartic.html +++ /dev/null @@ -1,84 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style quartic command -

    -

    angle_style quartic/omp command -

    -

    Syntax: -

    -
    angle_style quartic 
-
    -

    Examples: -

    -
    angle_style quartic
-angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 
-
    -

    Description: -

    -

    The quartic angle style uses the potential -

    -
    -
    -

    where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • theta0 (degrees) -
    • K2 (energy/radian^2) -
    • K3 (energy/radian^3) -
    • K4 (energy/radian^4) -
    -

    Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_sdk.html b/doc/doc2/angle_sdk.html deleted file mode 100644 index fa1b5f37dc..0000000000 --- a/doc/doc2/angle_sdk.html +++ /dev/null @@ -1,64 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style sdk command -

    -

    Syntax: -

    -
    angle_style sdk 
-
    -
    angle_style sdk/omp 
-
    -

    Examples: -

    -
    angle_style sdk
-angle_coeff 1 300.0 107.0 
-
    -

    Description: -

    -

    The sdk angle style is a combination of the harmonic angle potential, -

    -
    -
    -

    where theta0 is the equilibrium value of the angle and K a prefactor, -with the repulsive part of the non-bonded lj/sdk pair style -between the atoms 1 and 3. This angle potential is intended for -coarse grained MD simulations with the CMM parametrization using the -pair_style lj/sdk. Relative to the pair_style -lj/sdk, however, the energy is shifted by epsilon, to avoid sudden -jumps. Note that the usual 1/2 factor is included in K. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above: -

    -
    • K (energy/radian^2) -
    • theta0 (degrees) -
    -

    Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -The also required lj/sdk parameters will be extracted automatically -from the pair_style. -

    -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER-CG-CMM package. See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff, angle_style -harmonic, pair_style lj/sdk, -pair_style lj/sdk/coul/long -

    -

    Default: none -

    - diff --git a/doc/doc2/angle_style.html b/doc/doc2/angle_style.html deleted file mode 100644 index 97ea5e7d87..0000000000 --- a/doc/doc2/angle_style.html +++ /dev/null @@ -1,100 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style command -

    -

    Syntax: -

    -
    angle_style style 
-
    -
    • style = none or hybrid or charmm or class2 or cosine or cosine/squared or harmonic -
    -

    Examples: -

    -
    angle_style harmonic
-angle_style charmm
-angle_style hybrid harmonic cosine 
-
    -

    Description: -

    -

    Set the formula(s) LAMMPS uses to compute angle interactions between -triplets of atoms, which remain in force for the duration of the -simulation. The list of angle triplets is read in by a -read_data or read_restart command -from a data or restart file. -

    -

    Hybrid models where angles are computed using different angle -potentials can be setup using the hybrid angle style. -

    -

    The coefficients associated with a angle style can be specified in a -data or restart file or via the angle_coeff command. -

    -

    All angle potentials store their coefficient data in binary restart -files which means angle_style and angle_coeff -commands do not need to be re-specified in an input script that -restarts a simulation. See the read_restart -command for details on how to do this. The one exception is that -angle_style hybrid only stores the list of sub-styles in the restart -file; angle coefficients need to be re-specified. -

    -

    IMPORTANT NOTE: When both an angle and pair style is defined, the -special_bonds command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 3 bonded atoms. -

    -

    In the formulas listed for each angle style, theta is the angle -between the 3 atoms in the angle. -

    -
    - -

    Here is an alphabetic list of angle styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated angle_coeff command. -

    -

    Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of this -page. -

    - - -
    - -

    Restrictions: -

    -

    Angle styles can only be set for atom_styles that allow angles to be -defined. -

    -

    Most angle styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info on packages. -The doc pages for individual bond potentials tell if it is part of a -package. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: -

    -
    angle_style none 
-
    - diff --git a/doc/doc2/angle_table.html b/doc/doc2/angle_table.html deleted file mode 100644 index 9f136cd2df..0000000000 --- a/doc/doc2/angle_table.html +++ /dev/null @@ -1,163 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    angle_style table command -

    -

    angle_style table/omp command -

    -

    Syntax: -

    -
    angle_style table style N 
-
    -
    • style = linear or spline = method of interpolation -
    • N = use N values in table -
    -

    Examples: -

    -
    angle_style table linear 1000
-angle_coeff 3 file.table ENTRY1 
-
    -

    Description: -

    -

    Style table creates interpolation tables of length N from angle -potential and derivative values listed in a file(s) as a function of -angle The files are read by the angle_coeff -command. -

    -

    The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -N angles. During a simulation, these tables are used to interpolate -energy and force values on individual atoms as needed. The -interpolation is done in one of 2 styles: linear or spline. -

    -

    For the linear style, the angle is used to find 2 surrounding table -values from which an energy or its derivative is computed by linear -interpolation. -

    -

    For the spline style, a cubic spline coefficients are computed and -stored at each of the N values in the table. The angle is used to -find the appropriate set of coefficients which are used to evaluate a -cubic polynomial which computes the energy or derivative. -

    -

    The following coefficients must be defined for each angle type via the -angle_coeff command as in the example above. -

    -
    • filename -
    • keyword -
    -

    The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. -

    -
    - -

    The format of a tabulated file is as follows (without the -parenthesized comments): -

    -
    # Angle potential for harmonic (one or more comment or blank lines) 
-
    -
    HAM                           (keyword is the first text on line)
-N 181 FP 0 0 EQ 90.0          (N, FP, EQ parameters)
-                              (blank line)
-N 181 FP 0 0                  (N, FP parameters)
-1 0.0 200.5 2.5               (index, angle, energy, derivative)
-2 1.0 198.0 2.5
-...
-181 180.0 0.0 0.0 
-
    -

    A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -angle_coeff command. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. -

    -

    The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the angle_style table command. Let -Ntable = N in the angle_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and derivative -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual angles and their atoms. This means that if you -want the interpolation tables of length Ntable to match exactly what -is in the tabulated file (with effectively no preliminary -interpolation), you should set Ntable = Nfile. -

    -

    The "FP" parameter is optional. If used, it is followed by two values -fplo and fphi, which are the 2nd derivatives at the innermost and -outermost angle settings. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two -derivative values in the table. -

    -

    The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium angle value, which is used, for example, by the fix -shake command. If not used, the equilibrium angle is -set to 180.0. -

    -

    Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the angle value (in degrees), the 3rd value is the energy (in energy -units), and the 4th is -dE/d(theta) (also in energy units). The 3rd -term is the energy of the 3-atom configuration for the specified -angle. The last term is the derivative of the energy with respect to -the angle (in degrees, not radians). Thus the units of the last term -are still energy, not force. The angle values must increase from one -line to the next. The angle values must also begin with 0.0 and end -with 180.0, i.e. span the full range of possible angles. -

    -

    Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    angle_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/atom_modify.html b/doc/doc2/atom_modify.html deleted file mode 100644 index 7dc0ab5a74..0000000000 --- a/doc/doc2/atom_modify.html +++ /dev/null @@ -1,179 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS -Commands -
    - - - - - - -
    - -

    atom_modify command -

    -

    Syntax: -

    -
    atom_modify keyword values ... 
-
    -
    • one or more keyword/value pairs may be appended - -
    • keyword = id or map or first or sort - -
         id value = yes or no
-   map value = array or hash
-   first value = group-ID = group whose atoms will appear first in internal atom lists
-   sort values = Nfreq binsize
-     Nfreq = sort atoms spatially every this many time steps
-     binsize = bin size for spatial sorting (distance units) 
-
      - -
    -

    Examples: -

    -
    atom_modify map hash
-atom_modify map array sort 10000 2.0
-atom_modify first colloid 
-
    -

    Description: -

    -

    Modify certain attributes of atoms defined and stored within LAMMPS, -in addition to what is specified by the atom_style -command. The id and map keywords must be specified before a -simulation box is defined; other keywords can be specified any time. -

    -

    The id keyword determines whether non-zero atom IDs can be assigned -to each atom. If the value is yes, which is the default, IDs are -assigned, whether you use the create atoms or -read_data or read_restart -commands to initialize atoms. If the value is no the IDs for all -atoms are assumed to be 0. -

    -

    If atom IDs are used, they must all be positive integers. They should -also be unique, though LAMMPS does not check for this. Typically they -should also be consecutively numbered (from 1 to Natoms), though this -is not required. Molecular atom styles are those -that store bond topology information (styles bond, angle, molecular, -full). These styles require atom IDs since the IDs are used to encode -the topology. Some other LAMMPS commands also require the use of atom -IDs. E.g. some many-body pair styles use them to avoid double -computation of the I-J interaction between two atoms. -

    -

    The only reason not to use atom IDs is if you are running an atomic -simulation so large that IDs cannot be uniquely assigned. For a -default LAMMPS build this limit is 2^31 or about 2 billion atoms. -However, even in this case, you can use 64-bit atom IDs, allowing 2^63 -or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG -switch. This is described in Section 2.2 -of the manual. If atom IDs are not used, they must be specified as 0 -for all atoms, e.g. in a data or restart file. -

    -

    The map keyword determines how atom ID lookup is done for molecular -atom styles. Lookups are performed by bond (angle, etc) routines in -LAMMPS to find the local atom index associated with a global atom ID. -

    -

    When the array value is used, each processor stores a lookup table -of length N, where N is the largest atom ID in the system. This is a -fast, simple method for many simulations, but requires too much memory -for large simulations. The hash value uses a hash table to perform -the lookups. This can be slightly slower than the array method, but -its memory cost is proportional to the number of atoms owned by a -processor, i.e. N/P when N is the total number of atoms in the system -and P is the number of processors. -

    -

    When this setting is not specified in your input script, LAMMPS -creates a map, if one is needed, as an array or hash. See the -discussion of default values below for how LAMMPS chooses which kind -of map to build. Note that atomic systems do not normally need to -create a map. However, even in this case some LAMMPS commands will -create a map to find atoms (and then destroy it), or require a -permanent map. An example of the former is the velocity loop -all command, which uses a map when looping over all -atoms and insuring the same velocity values are assigned to an atom -ID, no matter which processor owns it. -

    -

    The first keyword allows a group to be specified whose -atoms will be maintained as the first atoms in each processor's list -of owned atoms. This in only useful when the specified group is a -small fraction of all the atoms, and there are other operations LAMMPS -is performing that will be sped-up significantly by being able to loop -over the smaller set of atoms. Otherwise the reordering required by -this option will be a net slow-down. The neigh_modify -include and comm_modify group -commands are two examples of commands that require this setting to -work efficiently. Several fixes, most notably time -integration fixes like fix nve, also take advantage of -this setting if the group they operate on is the group specified by -this command. Note that specifying "all" as the group-ID effectively -turns off the first option. -

    -

    It is OK to use the first keyword with a group that has not yet been -defined, e.g. to use the atom_modify first command at the beginning of -your input script. LAMMPS does not use the group until a simullation -is run. -

    -

    The sort keyword turns on a spatial sorting or reordering of atoms -within each processor's sub-domain every Nfreq timesteps. If -Nfreq is set to 0, then sorting is turned off. Sorting can improve -cache performance and thus speed-up a LAMMPS simulation, as discussed -in a paper by (Meloni). Its efficacy depends on the problem -size (atoms/processor), how quickly the system becomes disordered, and -various other factors. As a general rule, sorting is typically more -effective at speeding up simulations of liquids as opposed to solids. -In tests we have done, the speed-up can range from zero to 3-4x. -

    -

    Reordering is peformed every Nfreq timesteps during a dynamics run -or iterations during a minimization. More precisely, reordering -occurs at the first reneighboring that occurs after the target -timestep. The reordering is performed locally by each processor, -using bins of the specified binsize. If binsize is set to 0.0, -then a binsize equal to half the neighbor cutoff -distance (force cutoff plus skin distance) is used, which is a -reasonable value. After the atoms have been binned, they are -reordered so that atoms in the same bin are adjacent to each other in -the processor's 1d list of atoms. -

    -

    The goal of this procedure is for atoms to put atoms close to each -other in the processor's one-dimensional list of atoms that are also -near to each other spatially. This can improve cache performance when -pairwise intereractions and neighbor lists are computed. Note that if -bins are too small, there will be few atoms/bin. Likewise if bins are -too large, there will be many atoms/bin. In both cases, the goal of -cache locality will be undermined. -

    -

    IMPORTANT NOTE: Running a simulation with sorting on versus off should -not change the simulation results in a statistical sense. However, a -different ordering will induce round-off differences, which will lead -to diverging trajectories over time when comparing two simluations. -Various commands, particularly those which use random numbers -(e.g. velocity create, and fix -langevin), may generate (statistically identical) -results which depend on the order in which atoms are processed. The -order of atoms in a dump file will also typically change -if sorting is enabled. -

    -

    Restrictions: -

    -

    The first and sort options cannot be used together. Since sorting -is on by default, it will be turned off if the first keyword is -used with a group-ID that is not "all". -

    -

    Related commands: none -

    -

    Default: -

    -

    By default, id is yes. By default, atomic systems (no bond topology -info) do not use a map. For molecular systems (with bond topology -info), a map is used. The default map style is array if no atom ID is -larger than 1 million, otherwise the default is hash. By default, a -"first" group is not defined. By default, sorting is enabled with a -frequency of 1000 and a binsize of 0.0, which means the neighbor -cutoff will be used to set the bin size. -

    -
    - - - -

    (Meloni) Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007). -

    - diff --git a/doc/doc2/atom_style.html b/doc/doc2/atom_style.html deleted file mode 100644 index a8a9cc45d8..0000000000 --- a/doc/doc2/atom_style.html +++ /dev/null @@ -1,276 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    atom_style command -

    -

    Syntax: -

    -
    atom_style style args 
-
    -
    • style = angle or atomic or body or bond or charge or dipole or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or tri or template or hybrid - -
        args = none for any style except body and hybrid
-  body args = bstyle bstyle-args
-    bstyle = style of body particles
-    bstyle-args = additional arguments specific to the bstyle
-                  see the body doc page for details
-  template args = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
-  hybrid args = list of one or more sub-styles, each with their args 
-
      -
    • accelerated styles (with same args) = angle/cuda or angle/kk or atomic/cuda or atomic/kk or bond/kk or charge/cuda or charge/kk or full/cuda or full/kk or molecular/kk - - -
    -

    Examples: -

    -
    atom_style atomic
-atom_style bond
-atom_style full
-atom_style full/cuda
-atom_style body nparticle 2 10
-atom_style hybrid charge bond
-atom_style hybrid charge body nparticle 2 5
-atom_style template myMols 
-
    -

    Description: -

    -

    Define what style of atoms to use in a simulation. This determines -what attributes are associated with the atoms. This command must be -used before a simulation is setup via a read_data, -read_restart, or create_box -command. -

    -

    Once a style is assigned, it cannot be changed, so use a style general -enough to encompass all attributes. E.g. with style bond, angular -terms cannot be used or added later to the model. It is OK to use a -style more general than needed, though it may be slightly inefficient. -

    -

    The choice of style affects what quantities are stored by each atom, -what quantities are communicated between processors to enable forces -to be computed, and what quantities are listed in the data file read -by the read_data command. -

    -

    These are the additional attributes of each style and the typical -kinds of physical systems they are used to model. All styles store -coordinates, velocities, atom IDs and types. See the -read_data, create_atoms, and -set commands for info on how to set these various -quantities. -

    -
    - - - - - - - - - - - - - - - - - -
    angle bonds and angles bead-spring polymers with stiffness
    atomic only the default values coarse-grain liquids, solids, metals
    body mass, inertia moments, quaternion, angular momentum arbitrary bodies
    bond bonds bead-spring polymers
    charge charge atomic system with charges
    dipole charge and dipole moment system with dipolar particles
    electron charge and spin and eradius electronic force field
    ellipsoid shape, quaternion, angular momentum aspherical particles
    full molecular + charge bio-molecules
    line end points, angular velocity rigid bodies
    meso rho, e, cv SPH particles
    molecular bonds, angles, dihedrals, impropers uncharged molecules
    peri mass, volume mesocopic Peridynamic models
    smd volume, kernel diameter, contact radius, mass solid and fluid SPH particles
    sphere diameter, mass, angular velocity granular models
    template template index, template atom small molecules with fixed topology
    tri corner points, angular momentum rigid bodies
    wavepacket charge, spin, eradius, etag, cs_re, cs_im AWPMD -
    - -

    IMPORTANT NOTE: It is possible to add some attributes, such as a -molecule ID, to atom styles that do not have them via the fix -property/atom command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the fix -property/atom doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. -

    -

    All of the above styles define point particles, except the sphere, -ellipsoid, electron, peri, wavepacket, line, tri, and -body styles, which define finite-size particles. See Section_howto -14 for an overview of using finite-size -particle models with LAMMPS. -

    -

    All of the point-particle styles assign mass to particles on a -per-type basis, using the mass command, The finite-size -particle styles assign mass to individual particles on a per-particle -basis. -

    -

    For the sphere style, the particles are spheres and each stores a -per-particle diameter and mass. If the diameter > 0.0, the particle -is a finite-size sphere. If the diameter = 0.0, it is a point -particle. -

    -

    For the ellipsoid style, the particles are ellipsoids and each -stores a flag which indicates whether it is a finite-size ellipsoid or -a point particle. If it is an ellipsoid, it also stores a shape -vector with the 3 diamters of the ellipsoid and a quaternion 4-vector -with its orientation. -

    -

    For the electron style, the particles representing electrons are 3d -Gaussians with a specified position and bandwidth or uncertainty in -position, which is represented by the eradius = electron size. -

    -

    For the peri style, the particles are spherical and each stores a -per-particle mass and volume. -

    -

    The meso style is for smoothed particle hydrodynamics (SPH) -particles which store a density (rho), energy (e), and heat capacity -(cv). -

    -

    The smd style is for a general formulation of Smooth Particle -Hydrodynamics. Both fluids and solids can be modeled. Particles -store the mass and volume of an integration point, a kernel diameter -used for calculating the field variables (e.g. stress and deformation) -and a contact radius for calculating repulsive forces which prevent -individual physical bodies from penetretating each other. -

    -

    The wavepacket style is similar to electron, but the electrons may -consist of several Gaussian wave packets, summed up with coefficients -cs= (cs_re,cs_im). Each of the wave packets is treated as a separate -particle in LAMMPS, wave packets belonging to the same electron must -have identical etag values. -

    -

    For the line style, the particles are idealized line segments and -each stores a per-particle mass and length and orientation (i.e. the -end points of the line segment). -

    -

    For the tri style, the particles are planar triangles and each -stores a per-particle mass and size and orientation (i.e. the corner -points of the triangle). -

    -

    The template style allows molecular topolgy (bonds,angles,etc) to be -defined via a molecule template using the molecule -command. The template stores one or more molecules with a single copy -of the topology info (bonds,angles,etc) of each. Individual atoms -only store a template index and template atom to identify which -molecule and which atom-within-the-molecule they represent. Using the -template style instead of the bond, angle, molecular styles -can save memory for systems comprised of a large number of small -molecules, all of a single type (or small number of types). See the -paper by Grime and Voth, in (Grime), for examples of how this -can be advantageous for large-scale coarse-grained systems. -

    -

    IMPORTANT NOTE: When using the template style with a molecule -template that contains multiple molecules, you should -insure the atom types, bond types, angle_types, etc in all the -molecules are consistent. E.g. if one molecule represents H2O and -another CO2, then you probably do not want each molecule file to -define 2 atom types and a single bond type, because they will conflict -with each other when a mixture system of H2O and CO2 molecules is -defined, e.g. by the read_data command. Rather the -H2O molecule should define atom types 1 and 2, and bond type 1. And -the CO2 molecule should define atom types 3 and 4 (or atom types 3 and -2 if a single oxygen type is desired), and bond type 2. -

    -

    For the body style, the particles are arbitrary bodies with internal -attributes defined by the "style" of the bodies, which is specified by -the bstyle argument. Body particles can represent complex entities, -such as surface meshes of discrete points, collections of -sub-particles, deformable objects, etc. -

    -

    The body doc page descibes the body styles LAMMPS -currently supports, and provides more details as to the kind of body -particles they represent. For all styles, each body particle stores -moments of inertia and a quaternion 4-vector, so that its orientation -and position can be time integrated due to forces and torques. -

    -

    Note that there may be additional arguments required along with the -bstyle specification, in the atom_style body command. These -arguments are described in the body doc page. -

    -
    - -

    Typically, simulations require only a single (non-hybrid) atom style. -If some atoms in the simulation do not have all the properties defined -by a particular style, use the simplest style that defines all the -needed properties by any atom. For example, if some atoms in a -simulation are charged, but others are not, use the charge style. -If some atoms have bonds, but others do not, use the bond style. -

    -

    The only scenario where the hybrid style is needed is if there is no -single style which defines all needed properties of all atoms. For -example, if you want dipolar particles which will rotate due to -torque, you would need to use "atom_style hybrid sphere dipole". When -a hybrid style is used, atoms store and communicate the union of all -quantities implied by the individual styles. -

    -

    When using the hybrid style, you cannot combine the template style -with another molecular style that stores bond,angle,etc info on a -per-atom basis. -

    -

    LAMMPS can be extended with new atom styles as well as new body -styles; see this section. -

    -
    - -

    Styles with a cuda or kk suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    Note that other acceleration packages in LAMMPS, specifically the GPU, -USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom -styles. -

    -

    The accelerated styles are part of the USER-CUDA and KOKKOS packages -respectively. They are only enabled if LAMMPS was built with those -packages. See the Making LAMMPS section -for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restrictions: -

    -

    This command cannot be used after the simulation box is defined by a -read_data or create_box command. -

    -

    The angle, bond, full, molecular, and template styles are -part of the MOLECULE package. The line and tri styles are part -of the ASPHERE pacakge. The body style is part of the BODY package. -The dipole style is part of the DIPOLE package. The peri style is -part of the PERI package for Peridynamics. The electron style is -part of the USER-EFF package for electronic force -fields. The meso style is part of the USER-SPH -package for smoothed particle hydrodyanmics (SPH). See this PDF -guide to using SPH in LAMMPS. The -wavepacket style is part of the USER-AWPMD package for the -antisymmetrized wave packet MD method. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    read_data, pair_style -

    -

    Default: -

    -

    atom_style atomic -

    -
    - - - -

    (Grime) Grime and Voth, to appear in J Chem Theory & Computation -(2014). -

    - diff --git a/doc/doc2/balance.html b/doc/doc2/balance.html deleted file mode 100644 index 39acba35ea..0000000000 --- a/doc/doc2/balance.html +++ /dev/null @@ -1,360 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    balance command -

    -

    Syntax: -

    -
    balance thresh style args ... keyword value ... 
-
    -
    • thresh = imbalance threshhold that must be exceeded to perform a re-balance - -
    • one style/arg pair can be used (or multiple for x,y,z) - -
    • style = x or y or z or shift or rcb - -
        x args = uniform or Px-1 numbers between 0 and 1
-    uniform = evenly spaced cuts between processors in x dimension
-    numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
-    x can be specified together with y or z
-  y args = uniform or Py-1 numbers between 0 and 1
-    uniform = evenly spaced cuts between processors in y dimension
-    numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
-    y can be specified together with x or z
-  z args = uniform or Pz-1 numbers between 0 and 1
-    uniform = evenly spaced cuts between processors in z dimension
-    numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
-    z can be specified together with x or y
-  shift args = dimstr Niter stopthresh
-    dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
-    Niter = # of times to iterate within each dimension of dimstr sequence
-    stopthresh = stop balancing when this imbalance threshhold is reached
-  rcb args = none 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = out - -
        out value = filename
-    filename = write each processor's sub-domain to a file 
-
      - -
    -

    Examples: -

    -
    balance 0.9 x uniform y 0.4 0.5 0.6
-balance 1.2 shift xz 5 1.1
-balance 1.0 shift xz 5 1.1
-balance 1.1 rcb
-balance 1.0 shift x 20 1.0 out tmp.balance 
-
    -

    Description: -

    -

    This command adjusts the size and shape of processor sub-domains -within the simulation box, to attempt to balance the number of -particles and thus the computational cost (load) evenly across -processors. The load balancing is "static" in the sense that this -command performs the balancing once, before or between simulations. -The processor sub-domains will then remain static during the -subsequent run. To perform "dynamic" balancing, see the fix -balance command, which can adjust processor -sub-domain sizes and shapes on-the-fly during a run. -

    -

    Load-balancing is typically only useful if the particles in the -simulation box have a spatially-varying density distribution. E.g. a -model of a vapor/liquid interface, or a solid with an irregular-shaped -geometry containing void regions. In this case, the LAMMPS default of -dividing the simulation box volume into a regular-spaced grid of 3d -bricks, with one equal-volume sub-domain per procesor, may assign very -different numbers of particles per processor. This can lead to poor -performance when the simulation is run in parallel. -

    -

    Note that the processors command allows some control -over how the box volume is split across processors. Specifically, for -a Px by Py by Pz grid of processors, it allows choice of Px, Py, and -Pz, subject to the constraint that Px * Py * Pz = P, the total number -of processors. This is sufficient to achieve good load-balance for -some problems on some processor counts. However, all the processor -sub-domains will still have the same shape and same volume. -

    -

    The requested load-balancing operation is only performed if the -current "imbalance factor" in particles owned by each processor -exceeds the specified thresh parameter. The imbalance factor is -defined as the maximum number of particles owned by any processor, -divided by the average number of particles per processor. Thus an -imbalance factor of 1.0 is perfect balance. -

    -

    As an example, for 10000 particles running on 10 processors, if the -most heavily loaded processor has 1200 particles, then the factor is -1.2, meaning there is a 20% imbalance. Note that a re-balance can be -forced even if the current balance is perfect (1.0) be specifying a -thresh < 1.0. -

    -

    IMPORTANT NOTE: Balancing is performed even if the imbalance factor -does not exceed the thresh parameter if a "grid" style is specified -when the current partitioning is "tiled". The meaning of "grid" vs -"tiled" is explained below. This is to allow forcing of the -partitioning to "grid" so that the comm_style brick -command can then be used to replace a current comm_style -tiled setting. -

    -

    When the balance command completes, it prints statistics about the -result, including the change in the imbalance factor and the change in -the maximum number of particles on any processor. For "grid" methods -(defined below) that create a logical 3d grid of processors, the -positions of all cutting planes in each of the 3 dimensions (as -fractions of the box length) are also printed. -

    -

    IMPORTANT NOTE: This command attempts to minimize the imbalance -factor, as defined above. But depending on the method a perfect -balance (1.0) may not be achieved. For example, "grid" methods -(defined below) that create a logical 3d grid cannot achieve perfect -balance for many irregular distributions of particles. Likewise, if a -portion of the system is a perfect lattice, e.g. the intiial system is -generated by the create_atoms command, then "grid" -methods may be unable to achieve exact balance. This is because -entire lattice planes will be owned or not owned by a single -processor. -

    -

    IMPORTANT NOTE: The imbalance factor is also an estimate of the -maximum speed-up you can hope to achieve by running a perfectly -balanced simulation versus an imbalanced one. In the example above, -the 10000 particle simulation could run up to 20% faster if it were -perfectly balanced, versus when imbalanced. However, computational -cost is not strictly proportional to particle count, and changing the -relative size and shape of processor sub-domains may lead to -additional computational and communication overheads, e.g. in the PPPM -solver used via the kspace_style command. Thus -you should benchmark the run times of a simulation before and after -balancing. -

    -
    - -

    The method used to perform a load balance is specified by one of the -listed styles (or more in the case of x,y,z), which are -described in detail below. There are 2 kinds of styles. -

    -

    The x, y, z, and shift styles are "grid" methods which produce -a logical 3d grid of processors. They operate by changing the cutting -planes (or lines) between processors in 3d (or 2d), to adjust the -volume (area in 2d) assigned to each processor, as in the following 2d -diagram where processor sub-domains are shown and atoms are colored by -the processor that owns them. The leftmost diagram is the default -partitioning of the simulation box across processors (one sub-box for -each of 16 processors); the middle diagram is after a "grid" method -has been applied. -

    -
    -
    -

    The rcb style is a "tiling" method which does not produce a logical -3d grid of processors. Rather it tiles the simulation domain with -rectangular sub-boxes of varying size and shape in an irregular -fashion so as to have equal numbers of particles in each sub-box, as -in the rightmost diagram above. -

    -

    The "grid" methods can be used with either of the -comm_style command options, brick or tiled. The -"tiling" methods can only be used with comm_style -tiled. Note that it can be useful to use a "grid" -method with comm_style tiled to return the domain -partitioning to a logical 3d grid of processors so that "comm_style -brick" can afterwords be specified for subsequent run -commands. -

    -

    When a "grid" method is specified, the current domain partitioning can -be either a logical 3d grid or a tiled partitioning. In the former -case, the current logical 3d grid is used as a starting point and -changes are made to improve the imbalance factor. In the latter case, -the tiled partitioning is discarded and a logical 3d grid is created -with uniform spacing in all dimensions. This becomes the starting -point for the balancing operation. -

    -

    When a "tiling" method is specified, the current domain partitioning -("grid" or "tiled") is ignored, and a new partitioning is computed -from scratch. -

    -
    - -

    The x, y, and z styles invoke a "grid" method for balancing, as -described above. Note that any or all of these 3 styles can be -specified together, one after the other, but they cannot be used with -any other style. This style adjusts the position of cutting planes -between processor sub-domains in specific dimensions. Only the -specified dimensions are altered. -

    -

    The uniform argument spaces the planes evenly, as in the left -diagrams above. The numeric argument requires listing Ps-1 numbers -that specify the position of the cutting planes. This requires -knowing Ps = Px or Py or Pz = the number of processors assigned by -LAMMPS to the relevant dimension. This assignment is made (and the -Px, Py, Pz values printed out) when the simulation box is created by -the "create_box" or "read_data" or "read_restart" command and is -influenced by the settings of the processors -command. -

    -

    Each of the numeric values must be between 0 and 1, and they must be -listed in ascending order. They represent the fractional position of -the cutting place. The left (or lower) edge of the box is 0.0, and -the right (or upper) edge is 1.0. Neither of these values is -specified. Only the interior Ps-1 positions are specified. Thus is -there are 2 procesors in the x dimension, you specify a single value -such as 0.75, which would make the left processor's sub-domain 3x -larger than the right processor's sub-domain. -

    -
    - -

    The shift style invokes a "grid" method for balancing, as -described above. It changes the positions of cutting planes between -processors in an iterative fashion, seeking to reduce the imbalance -factor, similar to how the fix balance shift -command operates. -

    -

    The dimstr argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, -since there is no advantage to balancing on a dimension more than -once. You should normally only list dimensions where you expect there -to be a density variation in the particles. -

    -

    Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in dimstr, one dimension at a time. For a single -dimension, the balancing operation (described below) is iterated on up -to Niter times. After each dimension finishes, the imbalance factor -is re-computed, and the balancing operation halts if the stopthresh -criterion is met. -

    -

    A rebalance operation in a single dimension is performed using a -recursive multisectioning algorithm, where the position of each -cutting plane (line in 2d) in the dimension is adjusted independently. -This is similar to a recursive bisectioning for a single value, except -that the bounds used for each bisectioning take advantage of -information from neighboring cuts if possible. At each iteration, the -count of particles on either side of each plane is tallied. If the -counts do not match the target value for the plane, the position of -the cut is adjusted to be halfway between a low and high bound. The -low and high bounds are adjusted on each iteration, using new count -information, so that they become closer together over time. Thus as -the recustion progresses, the count of particles on either side of the -plane gets closer to the target value. -

    -

    Once the rebalancing is complete and final processor sub-domains -assigned, particles are migrated to their new owning processor, and -the balance procedure ends. -

    -

    IMPORTANT NOTE: At each rebalance operation, the bisectioning for each -cutting plane (line in 2d) typcially starts with low and high bounds -separated by the extent of a processor's sub-domain in one dimension. -The size of this bracketing region shrinks by 1/2 every iteration. -Thus if Niter is specified as 10, the cutting plane will typically -be positioned to 1 part in 1000 accuracy (relative to the perfect -target position). For Niter = 20, it will be accurate to 1 part in -a million. Thus there is no need ot set Niter to a large value. -LAMMPS will check if the threshold accuracy is reached (in a -dimension) is less iterations than Niter and exit early. However, -Niter should also not be set too small, since it will take roughly -the same number of iterations to converge even if the cutting plane is -initially close to the target value. -

    -
    - -

    The rcb style invokes a "tiled" method for balancing, as described -above. It performs a recursive coordinate bisectioning (RCB) of the -simulation domain. The basic idea is as follows. -

    -

    The simulation domain is cut into 2 boxes by an axis-aligned cut in -the longest dimension, leaving one new box on either side of the cut. -All the processors are also partitioned into 2 groups, half assigned -to the box on the lower side of the cut, and half to the box on the -upper side. (If the processor count is odd, one side gets an extra -processor.) The cut is positioned so that the number of atoms in the -lower box is exactly the number that the processors assigned to that -box should own for load balance to be perfect. This also makes load -balance for the upper box perfect. The positioning is done -iteratively, by a bisectioning method. Note that counting atoms on -either side of the cut requires communication between all processors -at each iteration. -

    -

    That is the procedure for the first cut. Subsequent cuts are made -recursively, in exactly the same manner. The subset of processors -assigned to each box make a new cut in the longest dimension of that -box, splitting the box, the subset of processsors, and the atoms in -the box in two. The recursion continues until every processor is -assigned a sub-box of the entire simulation domain, and owns the atoms -in that sub-box. -

    -
    - -

    The out keyword writes a text file to the specified filename with -the results of the balancing operation. The file contains the bounds -of the sub-domain for each processor after the balancing operation -completes. The format of the file is compatible with the -Pizza.py mdump tool which has support for manipulating and -visualizing mesh files. An example is shown here for a balancing by 4 -processors for a 2d problem: -

    -
    ITEM: TIMESTEP
-0
-ITEM: NUMBER OF NODES
-16
-ITEM: BOX BOUNDS
-0 10
-0 10
-0 10
-ITEM: NODES
-1 1 0 0 0
-2 1 5 0 0
-3 1 5 5 0
-4 1 0 5 0
-5 1 5 0 0
-6 1 10 0 0
-7 1 10 5 0
-8 1 5 5 0
-9 1 0 5 0
-10 1 5 5 0
-11 1 5 10 0
-12 1 10 5 0
-13 1 5 5 0
-14 1 10 5 0
-15 1 10 10 0
-16 1 5 10 0
-ITEM: TIMESTEP
-0
-ITEM: NUMBER OF SQUARES
-4
-ITEM: SQUARES
-1 1 1 2 3 4
-2 1 5 6 7 8
-3 1 9 10 11 12
-4 1 13 14 15 16 
-
    -

    The coordinates of all the vertices are listed in the NODES section, 5 -per processor. Note that the 4 sub-domains share vertices, so there -will be duplicate nodes in the list. -

    -

    The "SQUARES" section lists the node IDs of the 4 vertices in a -rectangle for each processor (1 to 4). -

    -

    For a 3d problem, the syntax is similar with 8 vertices listed for -each processor, instead of 4, and "SQUARES" replaced by "CUBES". -

    -
    - -

    Restrictions: -

    -

    For 2d simulations, the z style cannot be used. Nor can a "z" -appear in dimstr for the shift style. -

    -

    Related commands: -

    -

    processors, fix balance -

    -

    Default: none -

    - diff --git a/doc/doc2/body.html b/doc/doc2/body.html deleted file mode 100644 index 3d610764d2..0000000000 --- a/doc/doc2/body.html +++ /dev/null @@ -1,163 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    Body particles -

    -

    Overview: -

    -

    This doc page is not about a LAMMPS input script command, but about -body particles, which are generalized finite-size particles. -Individual body particles can represent complex entities, such as -surface meshes of discrete points, collections of sub-particles, -deformable objects, etc. Note that other kinds of finite-size -spherical and aspherical particles are also supported by LAMMPS, such -as spheres, ellipsoids, line segments, and triangles, but they are -simpler entities that body particles. See Section_howto -14 for a general overview of all these -particle types. -

    -

    Body particles are used via the atom_style body -command. It takes a body style as an argument. The current body -styles supported by LAMMPS are as follows. The name in the first -column is used as the bstyle argument for the atom_style -body command. -

    -
    -
    nparticle rigid body with N sub-particles -
    - -

    The body style determines what attributes are stored for each body and -thus how they can be used to compute pairwise body/body or -bond/non-body (point particle) interactions. More details of each -style are described below. -

    -

    We hope to add more styles in the future. See Section_modify -12 for details on how to add a new body -style to the code. -

    -
    - -

    When to use body particles: -

    -

    You should not use body particles to model a rigid body made of -simpler particles (e.g. point, sphere, ellipsoid, line segment, -triangular particles), if the interaction between pairs of rigid -bodies is just the summation of pairwise interactions between the -simpler particles. LAMMPS already supports this kind of model via the -fix rigid command. Any of the numerous pair styles -that compute interactions between simpler particles can be used. The -fix rigid command time integrates the motion of the -rigid bodies. All of the standard LAMMPS commands for thermostatting, -adding constraints, performing output, etc will operate as expected on -the simple particles. -

    -

    By contrast, when body particles are used, LAMMPS treats an entire -body as a single particle for purposes of computing pairwise -interactions, building neighbor lists, migrating particles between -processors, outputting particles to a dump file, etc. This means that -interactions between pairs of bodies or between a body and non-body -(point) particle need to be encoded in an appropriate pair style. If -such a pair style were to mimic the fix rigid model, -it would need to loop over the entire collection of interactions -between pairs of simple particles within the two bodies, each time a -single body/body interaction was computed. -

    -

    Thus it only makes sense to use body particles and develop such a pair -style, when particle/particle interactions are more complex than what -the fix rigid command can already calculate. For -example, if particles have one or more of the following attributes: -

    -
    • represented by a surface mesh -
    • represented by a collection of geometric entities (e.g. planes + spheres) -
    • deformable -
    • internal stress that induces fragmentation -
    -

    then the interaction between pairs of particles is likely to be more -complex than the summation of simple sub-particle interactions. An -example is contact or frictional forces between particles with planar -sufaces that inter-penetrate. -

    -

    These are additional LAMMPS commands that can be used with body -particles of different styles -

    -
    - - -
    fix nve/body integrate motion of a body particle
    compute body/local store sub-particle attributes of a body particle
    dump local output sub-particle attributes of a body particle -
    - -

    The pair styles defined for use with specific body styles are listed -in the sections below. -

    -
    - -

    Specifics of body style nparticle: -

    -

    The nparticle body style represents body particles as a rigid body -with a variable number N of sub-particles. It is provided as a -vanillia, prototypical example of a body particle, although as -mentioned above, the fix rigid command already -duplicates its functionality. -

    -

    The atom_style body command for this body style takes two additional -arguments: -

    -
    atom_style body nparticle Nmin Nmax
-Nmin = minimum # of sub-particles in any body in the system
-Nmax = maximum # of sub-particles in any body in the system 
-
    -

    The Nmin and Nmax arguments are used to bound the size of data -structures used internally by each particle. -

    -

    When the read_data command reads a data file for this -body style, the following information must be provided for each entry -in the Bodies section of the data file: -

    -
    atom-ID 1 M
-N
-ixx iyy izz ixy ixz iyz x1 y1 z1 ...
-...
-... xN yN zN 
-
    -

    N is the number of sub-particles in the body particle. M = 6 + 3*N. -The integer line has a single value N. The floating point line(s) -list 6 moments of inertia followed by the coordinates of the N -sub-particles (x1 to zN) as 3N values on as many lines as required. -Note that this in not N lines, but 10 values per line; see the -read_data command for details. The 6 moments of -inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with -the current orientation of the rigid body around its center of mass. -The values are with respect to the simulation box XYZ axes, not with -respect to the prinicpal axes of the rigid body itself. LAMMPS -performs the latter calculation internally. The coordinates of each -sub-particle are specified as its x,y,z displacement from the -center-of-mass of the body particle. The center-of-mass position of -the particle is specified by the x,y,z values in the Atoms section -of the data file. -

    -

    The pair_style body command can be used with this -body style to compute body/body and body/non-body interactions. -

    -

    For output purposes via the compute -body/local and dump local -commands, this body style produces one datum for each of the N -sub-particles in a body particle. The datum has 3 values: -

    -
    1 = x position of sub-particle
-2 = y position of sub-particle
-3 = z position of sub-particle 
-
    -

    These values are the current position of the sub-particle within the -simulation domain, not a displacement from the center-of-mass (COM) of -the body particle itself. These values are calculated using the -current COM and orientiation of the body particle. -

    - diff --git a/doc/doc2/bond_class2.html b/doc/doc2/bond_class2.html deleted file mode 100644 index 2c1611d443..0000000000 --- a/doc/doc2/bond_class2.html +++ /dev/null @@ -1,88 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style class2 command -

    -

    bond_style class2/omp command -

    -

    Syntax: -

    -
    bond_style class2 
-
    -

    Examples: -

    -
    bond_style class2
-bond_coeff 1 1.0 100.0 80.0 80.0 
-
    -

    Description: -

    -

    The class2 bond style uses the potential -

    -
    -
    -

    where r0 is the equilibrium bond distance. -

    -

    See (Sun) for a description of the COMPASS class2 force field. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • R0 (distance) -
    • K2 (energy/distance^2) -
    • K3 (energy/distance^3) -
    • K4 (energy/distance^4) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the CLASS2 -package. See the Making LAMMPS section -for more info on packages. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    -
    - - - -

    (Sun) Sun, J Phys Chem B 102, 7338-7364 (1998). -

    - diff --git a/doc/doc2/bond_coeff.html b/doc/doc2/bond_coeff.html deleted file mode 100644 index 4d6fb4d94d..0000000000 --- a/doc/doc2/bond_coeff.html +++ /dev/null @@ -1,100 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_coeff command -

    -

    Syntax: -

    -
    bond_coeff N args 
-
    -
    • N = bond type (see asterisk form below) -
    • args = coefficients for one or more bond types -
    -

    Examples: -

    -
    bond_coeff 5 80.0 1.2
-bond_coeff * 30.0 1.5 1.0 1.0
-bond_coeff 1*4 30.0 1.5 1.0 1.0
-bond_coeff 1 harmonic 200.0 1.0 
-
    -

    Description: -

    -

    Specify the bond force field coefficients for one or more bond types. -The number and meaning of the coefficients depends on the bond style. -Bond coefficients can also be set in the data file read by the -read_data command or in a restart file. -

    -

    N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple bond types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of bond types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). -

    -

    Note that using a bond_coeff command can override a previous setting -for the same bond type. For example, these commands set the coeffs -for all bond types, then overwrite the coeffs for just bond type 2: -

    -
    bond_coeff * 100.0 1.2
-bond_coeff 2 200.0 1.2 
-
    -

    A line in a data file that specifies bond coefficients uses the exact -same format as the arguments of the bond_coeff command in an input -script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Bond Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as -

    -
    5 80.0 1.2 
-
    -
    - -

    Here is an alphabetic list of bond styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated bond_coeff command. -

    -

    Note that here are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of this -page. -

    - - -
    - -

    Restrictions: -

    -

    This command must come after the simulation box is defined by a -read_data, read_restart, or -create_box command. -

    -

    A bond style must be defined before any bond coefficients are set, -either in the input script or in a data file. -

    -

    Related commands: -

    -

    bond_style -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_fene.html b/doc/doc2/bond_fene.html deleted file mode 100644 index e75edad892..0000000000 --- a/doc/doc2/bond_fene.html +++ /dev/null @@ -1,96 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style fene command -

    -

    bond_style fene/kk command -

    -

    bond_style fene/omp command -

    -

    Syntax: -

    -
    bond_style fene 
-
    -

    Examples: -

    -
    bond_style fene
-bond_coeff 1 30.0 1.5 1.0 1.0 
-
    -

    Description: -

    -

    The fene bond style uses the potential -

    -
    -
    -

    to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first -term is attractive, the 2nd Lennard-Jones term is repulsive. The -first term extends to R0, the maximum extent of the bond. The 2nd -term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy/distance^2) -
    • R0 (distance) -
    • epsilon (energy) -
    • sigma (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    You typically should specify special_bonds fene -or special_bonds lj/coul 0 1 1 to use this bond -style. LAMMPS will issue a warning it that's not the case. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    -
    - - - -

    (Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990). -

    - diff --git a/doc/doc2/bond_fene_expand.html b/doc/doc2/bond_fene_expand.html deleted file mode 100644 index db6cc88ae2..0000000000 --- a/doc/doc2/bond_fene_expand.html +++ /dev/null @@ -1,99 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style fene/expand command -

    -

    bond_style fene/expand/omp command -

    -

    Syntax: -

    -
    bond_style fene/expand 
-
    -

    Examples: -

    -
    bond_style fene/expand
-bond_coeff 1 30.0 1.5 1.0 1.0 0.5 
-
    -

    Description: -

    -

    The fene/expand bond style uses the potential -

    -
    -
    -

    to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first -term is attractive, the 2nd Lennard-Jones term is repulsive. -

    -

    The fene/expand bond style is similar to fene except that an extra -shift factor of delta (positive or negative) is added to r to -effectively change the bead size of the bonded atoms. The first term -now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma -+ delta. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy/distance^2) -
    • R0 (distance) -
    • epsilon (energy) -
    • sigma (distance) -
    • delta (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    You typically should specify special_bonds fene -or special_bonds lj/coul 0 1 1 to use this bond -style. LAMMPS will issue a warning it that's not the case. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    -
    - - - -

    (Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990). -

    - diff --git a/doc/doc2/bond_harmonic.html b/doc/doc2/bond_harmonic.html deleted file mode 100644 index f3738011b7..0000000000 --- a/doc/doc2/bond_harmonic.html +++ /dev/null @@ -1,81 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style harmonic command -

    -

    bond_style harmonic/kk command -

    -

    bond_style harmonic/omp command -

    -

    Syntax: -

    -
    bond_style harmonic 
-
    -

    Examples: -

    -
    bond_style harmonic
-bond_coeff 5 80.0 1.2 
-
    -

    Description: -

    -

    The harmonic bond style uses the potential -

    -
    -
    -

    where r0 is the equilibrium bond distance. Note that the usual 1/2 -factor is included in K. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy/distance^2) -
    • r0 (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_harmonic_shift.html b/doc/doc2/bond_harmonic_shift.html deleted file mode 100644 index 04b686a1ab..0000000000 --- a/doc/doc2/bond_harmonic_shift.html +++ /dev/null @@ -1,85 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style harmonic/shift command -

    -

    bond_style harmonic/shift/omp command -

    -

    Syntax: -

    -
    bond_style harmonic/shift 
-
    -

    Examples: -

    -
    bond_style harmonic/shift
-bond_coeff 5 10.0 0.5 1.0 
-
    -

    Description: -

    -

    The harmonic/shift bond style is a shifted harmonic bond that uses -the potential -

    -
    -
    -

    where r0 is the equilibrium bond distance, and rc the critical distance. -The potential is -Umin at r0 and zero at rc. The spring constant is -k = Umin / [ 2 (r0-rc)^2]. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • Umin (energy) -
    -
    • r0 (distance) -
    -
    • rc (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds, -bond_harmonic -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_harmonic_shift_cut.html b/doc/doc2/bond_harmonic_shift_cut.html deleted file mode 100644 index 9240cd1320..0000000000 --- a/doc/doc2/bond_harmonic_shift_cut.html +++ /dev/null @@ -1,84 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style harmonic/shift/cut command -

    -

    bond_style harmonic/shift/cut/omp command -

    -

    Syntax: -

    -
    bond_style harmonic/shift/cut 
-
    -

    Examples: -

    -
    bond_style harmonic/shift/cut
-bond_coeff 5 10.0 0.5 1.0 
-
    -

    Description: -

    -

    The harmonic/shift/cut bond style is a shifted harmonic bond that -uses the potential -

    -
    -
    -

    where r0 is the equilibrium bond distance, and rc the critical distance. -The bond potential is zero for distances r > rc. The potential is -Umin -at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)^2]. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • Umin (energy) -
    • r0 (distance) -
    • rc (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds, -bond_harmonic, -bond_harmonicshift -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_hybrid.html b/doc/doc2/bond_hybrid.html deleted file mode 100644 index 1477766841..0000000000 --- a/doc/doc2/bond_hybrid.html +++ /dev/null @@ -1,79 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style hybrid command -

    -

    Syntax: -

    -
    bond_style hybrid style1 style2 ... 
-
    -
    • style1,style2 = list of one or more bond styles -
    -

    Examples: -

    -
    bond_style hybrid harmonic fene
-bond_coeff 1 harmonic 80.0 1.2
-bond_coeff 2* fene 30.0 1.5 1.0 1.0 
-
    -

    Description: -

    -

    The hybrid style enables the use of multiple bond styles in one -simulation. A bond style is assigned to each bond type. For example, -bonds in a polymer flow (of bond type 1) could be computed with a -fene potential and bonds in the wall boundary (of bond type 2) could -be computed with a harmonic potential. The assignment of bond type -to style is made via the bond_coeff command or in -the data file. -

    -

    In the bond_coeff commands, the name of a bond style must be added -after the bond type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 bond_coeff -commands set bonds of bond type 1 to be computed with a harmonic -potential with coefficients 80.0, 1.2 for K, r0. All other bond types -(2-N) are computed with a fene potential with coefficients 30.0, -1.5, 1.0, 1.0 for K, R0, epsilon, sigma. -

    -

    If bond coefficients are specified in the data file read via the -read_data command, then the same rule applies. -E.g. "harmonic" or "fene" must be added after the bond type, for each -line in the "Bond Coeffs" section, e.g. -

    -
    Bond Coeffs 
-
    -
    1 harmonic 80.0 1.2
-2 fene 30.0 1.5 1.0 1.0
-... 
-
    -

    A bond style of none with no additional coefficients can be used in -place of a bond style, either in a input script bond_coeff command or -in the data file, if you desire to turn off interactions for specific -bond types. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Unlike other bond styles, the hybrid bond style does not store bond -coefficient info for individual sub-styles in a binary restart -files. Thus when retarting a simulation from a restart -file, you need to re-specify bond_coeff commands. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_morse.html b/doc/doc2/bond_morse.html deleted file mode 100644 index 38fd439571..0000000000 --- a/doc/doc2/bond_morse.html +++ /dev/null @@ -1,80 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style morse command -

    -

    bond_style morse/omp command -

    -

    Syntax: -

    -
    bond_style morse 
-
    -

    Examples: -

    -
    bond_style morse
-bond_coeff 5 1.0 2.0 1.2 
-
    -

    Description: -

    -

    The morse bond style uses the potential -

    -
    -
    -

    where r0 is the equilibrium bond distance, alpha is a stiffness -parameter, and D determines the depth of the potential well. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • D (energy) -
    • alpha (inverse distance) -
    • r0 (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_none.html b/doc/doc2/bond_none.html deleted file mode 100644 index ed59eca4c2..0000000000 --- a/doc/doc2/bond_none.html +++ /dev/null @@ -1,34 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style none command -

    -

    Syntax: -

    -
    bond_style none 
-
    -

    Examples: -

    -
    bond_style none 
-
    -

    Description: -

    -

    Using a bond style of none means bond forces are not computed, even if -pairs of bonded atoms were listed in the data file read by the -read_data command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_nonlinear.html b/doc/doc2/bond_nonlinear.html deleted file mode 100644 index f920a20e0e..0000000000 --- a/doc/doc2/bond_nonlinear.html +++ /dev/null @@ -1,86 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style nonlinear command -

    -

    bond_style nonlinear/omp command -

    -

    Syntax: -

    -
    bond_style nonlinear 
-
    -

    Examples: -

    -
    bond_style nonlinear
-bond_coeff 2 100.0 1.1 1.4 
-
    -

    Description: -

    -

    The nonlinear bond style uses the potential -

    -
    -
    -

    to define an anharmonic spring (Rector) of equilibrium -length r0 and maximum extension lamda. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • epsilon (energy) -
    • r0 (distance) -
    • lamda (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    -
    - - - -

    (Rector) Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994). -

    - diff --git a/doc/doc2/bond_quartic.html b/doc/doc2/bond_quartic.html deleted file mode 100644 index 403af0aa18..0000000000 --- a/doc/doc2/bond_quartic.html +++ /dev/null @@ -1,119 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style quartic command -

    -

    bond_style quartic/omp command -

    -

    Syntax: -

    -
    bond_style quartic 
-
    -

    Examples: -

    -
    bond_style quartic
-bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 
-
    -

    Description: -

    -

    The quartic bond style uses the potential -

    -
    -
    -

    to define a bond that can be broken as the simulation proceeds (e.g. -due to a polymer being stretched). The sigma and epsilon used in the -LJ portion of the formula are both set equal to 1.0 by LAMMPS. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy/distance^4) -
    • B1 (distance) -
    • B2 (distance) -
    • Rc (distance) -
    • U0 (energy) -
    -

    This potential was constructed to mimic the FENE bond potential for -coarse-grained polymer chains. When monomers with sigma = epsilon = -1.0 are used, the following choice of parameters gives a quartic -potential that looks nearly like the FENE potential: K = 1200, B1 = --0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters -can be specified using the bond_coeff command, but -you will need to choose them carefully so they form a suitable bond -potential. -

    -

    Rc is the cutoff length at which the bond potential goes smoothly to a -local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" -the bond, which means two things. First, the bond potential is turned -off by setting its type to 0, and is no longer computed. Second, a -pairwise interaction between the two atoms is turned on, since they -are no longer bonded. -

    -

    LAMMPS does the second task via a computational sleight-of-hand. It -subtracts the pairwise interaction as part of the bond computation. -When the bond breaks, the subtraction stops. For this to work, the -pairwise interaction must always be computed by the -pair_style command, whether the bond is broken or -not. This means that special_bonds must be set -to 1,1,1, as indicated as a restriction below. -

    -

    Note that when bonds are dumped to a file via the dump -local command, bonds with type 0 are not included. The -delete_bonds command can also be used to query the -status of broken bonds or permanently delete them, e.g.: -

    -
    delete_bonds all stats
-delete_bonds all bond 0 remove 
-
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    The quartic style requires that special_bonds -parameters be set to 1,1,1. Three- and four-body interactions (angle, -dihedral, etc) cannot be used with quartic bonds. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    - diff --git a/doc/doc2/bond_style.html b/doc/doc2/bond_style.html deleted file mode 100644 index 135676886d..0000000000 --- a/doc/doc2/bond_style.html +++ /dev/null @@ -1,109 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style command -

    -

    Syntax: -

    -
    bond_style style args 
-
    -
    • style = none or hybrid or class2 or fene or fene/expand or harmonic or morse or nonlinear or quartic -
    -
      args = none for any style except hybrid
-  hybrid args = list of one or more styles 
-
    -

    Examples: -

    -
    bond_style harmonic
-bond_style fene
-bond_style hybrid harmonic fene 
-
    -

    Description: -

    -

    Set the formula(s) LAMMPS uses to compute bond interactions between -pairs of atoms. In LAMMPS, a bond differs from a pairwise -interaction, which are set via the pair_style -command. Bonds are defined between specified pairs of atoms and -remain in force for the duration of the simulation (unless the bond -breaks which is possible in some bond potentials). The list of bonded -atoms is read in by a read_data or -read_restart command from a data or restart file. -By contrast, pair potentials are typically defined between all pairs -of atoms within a cutoff distance and the set of active interactions -changes over time. -

    -

    Hybrid models where bonds are computed using different bond potentials -can be setup using the hybrid bond style. -

    -

    The coefficients associated with a bond style can be specified in a -data or restart file or via the bond_coeff command. -

    -

    All bond potentials store their coefficient data in binary restart -files which means bond_style and bond_coeff commands -do not need to be re-specified in an input script that restarts a -simulation. See the read_restart command for -details on how to do this. The one exception is that bond_style -hybrid only stores the list of sub-styles in the restart file; bond -coefficients need to be re-specified. -

    -

    IMPORTANT NOTE: When both a bond and pair style is defined, the -special_bonds command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 2 bonded atoms. -

    -

    In the formulas listed for each bond style, r is the distance -between the 2 atoms in the bond. -

    -
    - -

    Here is an alphabetic list of bond styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated bond_coeff command. -

    -

    Note that there are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of this -page. -

    - - -
    - -

    Restrictions: -

    -

    Bond styles can only be set for atom styles that allow bonds to be -defined. -

    -

    Most bond styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info on packages. -The doc pages for individual bond potentials tell if it is part of a -package. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: -

    -

    bond_style none -

    - diff --git a/doc/doc2/bond_table.html b/doc/doc2/bond_table.html deleted file mode 100644 index fb92e239fe..0000000000 --- a/doc/doc2/bond_table.html +++ /dev/null @@ -1,160 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    bond_style table command -

    -

    bond_style table/omp command -

    -

    Syntax: -

    -
    bond_style table style N 
-
    -
    • style = linear or spline = method of interpolation -
    • N = use N values in table -
    -

    Examples: -

    -
    bond_style table linear 1000
-bond_coeff 1 file.table ENTRY1 
-
    -

    Description: -

    -

    Style table creates interpolation tables of length N from bond -potential and force values listed in a file(s) as a function of bond -length. The files are read by the bond_coeff -command. -

    -

    The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and force values at each of N -distances. During a simulation, these tables are used to interpolate -energy and force values as needed. The interpolation is done in one -of 2 styles: linear or spline. -

    -

    For the linear style, the bond length is used to find 2 surrounding -table values from which an energy or force is computed by linear -interpolation. -

    -

    For the spline style, a cubic spline coefficients are computed and -stored at each of the N values in the table. The bond length is -used to find the appropriate set of coefficients which are used to -evaluate a cubic polynomial which computes the energy or force. -

    -

    The following coefficients must be defined for each bond type via the -bond_coeff command as in the example above. -

    -
    • filename -
    • keyword -
    -

    The filename specifies a file containing tabulated energy and force -values. The keyword specifies a section of the file. The format of -this file is described below. -

    -
    - -

    The format of a tabulated file is as follows (without the -parenthesized comments): -

    -
    # Bond potential for harmonic (one or more comment or blank lines) 
-
    -
    HAM                           (keyword is the first text on line)
-N 101 FP 0 0 EQ 0.5           (N, FP, EQ  parameters)
-                              (blank line)
-1 0.00 338.0000 1352.0000     (index, bond-length, energy, force)
-2 0.01 324.6152 1324.9600
-...
-101 1.00 338.0000 -1352.0000 
-
    -

    A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -bond_coeff command. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. -

    -

    The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the bond_style table command. Let -Ntable = N in the bond_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and force -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual bond lengths. This means that if you want the -interpolation tables of length Ntable to match exactly what is in the -tabulated file (with effectively no preliminary interpolation), you -should set Ntable = Nfile. -

    -

    The "FP" parameter is optional. If used, it is followed by two values -fplo and fphi, which are the derivatives of the force at the innermost -and outermost bond lengths. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two force -values in the table. -

    -

    The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium bond length, which is used, for example, by the fix -shake command. If not used, the equilibrium bond -length is set to 0.0. -

    -

    Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the bond length r (in distance units), the 3rd value is the energy (in -energy units), and the 4th is the force (in force units). The bond -lengths must range from a LO value to a HI value, and increase from -one line to the next. If the actual bond length is ever smaller than -the LO value or larger than the HI value, then the bond energy and -force is evaluated as if the bond were the LO or HI length. -

    -

    Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This bond style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    bond_coeff, delete_bonds -

    -

    Default: none -

    - diff --git a/doc/doc2/boundary.html b/doc/doc2/boundary.html deleted file mode 100644 index a427194ee1..0000000000 --- a/doc/doc2/boundary.html +++ /dev/null @@ -1,106 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    boundary command -

    -

    Syntax: -

    -
    boundary x y z 
-
    -
    • x,y,z = p or s or f or m, one or two letters - -
        p is periodic
-  f is non-periodic and fixed
-  s is non-periodic and shrink-wrapped
-  m is non-periodic and shrink-wrapped with a minimum value 
-
      - -
    -

    Examples: -

    -
    boundary p p f
-boundary p fs p
-boundary s f fm 
-
    -

    Description: -

    -

    Set the style of boundaries for the global simulation box in each -dimension. A single letter assigns the same style to both the lower -and upper face of the box. Two letters assigns the first style to the -lower face and the second style to the upper face. The initial size -of the simulation box is set by the read_data, -read_restart, or create_box -commands. -

    -

    The style p means the box is periodic, so that particles interact -across the boundary, and they can exit one end of the box and re-enter -the other end. A periodic dimension can change in size due to -constant pressure boundary conditions or box deformation (see the fix -npt and fix deform commands). The p -style must be applied to both faces of a dimension. -

    -

    The styles f, s, and m mean the box is non-periodic, so that -particles do not interact across the boundary and do not move from one -side of the box to the other. -

    -

    For style f, the position of the face is fixed. If an atom moves -outside the face it will be deleted on the next timestep that -reneighboring occurs. This will typically generate an error unless -you have set the thermo_modify lost option to -allow for lost atoms. -

    -

    For style s, the position of the face is set so as to encompass the -atoms in that dimension (shrink-wrapping), no matter how far they -move. -

    -

    For style m, shrink-wrapping occurs, but is bounded by the value -specified in the data or restart file or set by the -create_box command. For example, if the upper z -face has a value of 50.0 in the data file, the face will always be -positioned at 50.0 or above, even if the maximum z-extent of all the -atoms becomes less than 50.0. This can be useful if you start a -simulation with an empty box or if you wish to leave room on one side -of the box, e.g. for atoms to evaporate from a surface. -

    -

    For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension -of a tilt factor (e.g. y for xy) is periodic, then the periodicity is -enforced with the tilt factor offset. If the 1st dimension is -shrink-wrapped, then the shrink wrapping is applied to the tilted box -face, to encompass the atoms. E.g. for a positive xy tilt, the xlo -and xhi faces of the box are planes tilting in the +y direction as y -increases. These tilted planes are shrink-wrapped around the atoms to -determine the x extent of the box. -

    -

    See Section_howto 12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used -triclinic representations. -

    -

    Restrictions: -

    -

    This command cannot be used after the simulation box is defined by a -read_data or create_box command or -read_restart command. See the -change_box command for how to change the simulation -box boundaries after it has been defined. -

    -

    For 2d simulations, the z dimension must be periodic. -

    -

    Related commands: -

    -

    See the thermo_modify command for a discussion -of lost atoms. -

    -

    Default: -

    -
    boundary p p p 
-
    - diff --git a/doc/doc2/box.html b/doc/doc2/box.html deleted file mode 100644 index 162087c7ff..0000000000 --- a/doc/doc2/box.html +++ /dev/null @@ -1,69 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    box command -

    -

    Syntax: -

    -
    box keyword value ... 
-
    -
    • one or more keyword/value pairs may be appended - -
    • keyword = tilt - -
        tilt value = small or large 
-
      - -
    -

    Examples: -

    -
    box tilt large
-box tilt small 
-
    -

    Description: -

    -

    Set attributes of the simulation box. -

    -

    For triclinic (non-orthogonal) simulation boxes, the tilt keyword -allows simulation domains to be created with arbitrary tilt factors, -e.g. via the create_box or -read_data commands. Tilt factors determine how -skewed the triclinic box is; see this -section of the manual for a discussion of -triclinic boxes in LAMMPS. -

    -

    LAMMPS normally requires that no tilt factor can skew the box more -than half the distance of the parallel box length, which is the 1st -dimension in the tilt factor (x for xz). If tilt is set to -small, which is the default, then an error will be -generated if a box is created which exceeds this limit. If tilt -is set to large, then no limit is enforced. You can create -a box with any tilt factors you wish. -

    -

    Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. -

    -

    Restrictions: -

    -

    This command cannot be used after the simulation box is defined by a -read_data or create_box command or -read_restart command. -

    -

    Related commands: none -

    -

    Default: -

    -

    The default value is tilt = small. -

    - diff --git a/doc/doc2/change_box.html b/doc/doc2/change_box.html deleted file mode 100644 index c40a3f588b..0000000000 --- a/doc/doc2/change_box.html +++ /dev/null @@ -1,342 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    change_box command -

    -

    Syntax: -

    -
    change_box group-ID parameter args ... keyword args ... 
-
    -
    • group-ID = ID of group of atoms to (optionally) displace - -
    • one or more parameter/arg pairs may be appended - -
      parameter = x or y or z or xy or xz or yz or boundary or ortho or triclinic or set or remap
-  x, y, z args = style value(s)
-    style = final or delta or scale or volume
-      final values = lo hi
-        lo hi = box boundaries after displacement (distance units)
-      delta values = dlo dhi
-        dlo dhi = change in box boundaries after displacement (distance units)
-      scale values = factor
-        factor = multiplicative factor for change in box length after displacement
-      volume value = none = adjust this dim to preserve volume of system
-  xy, xz, yz args = style value
-    style = final or delta
-      final value = tilt
-        tilt = tilt factor after displacement (distance units)
-      delta value = dtilt
-        dtilt = change in tilt factor after displacement (distance units)
-  boundary args = x y z
-    x,y,z = p or s or f or m, one or two letters
-    p is periodic
-    f is non-periodic and fixed
-    s is non-periodic and shrink-wrapped
-    m is non-periodic and shrink-wrapped with a minimum value
-  ortho args = none = change box to orthogonal
-  triclinic args = none = change box to triclinic
-  set args = none = store state of current box
-  remap args = none = remap atom coords from last saved state to current box 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = units - -
        units value = lattice or box
-    lattice = distances are defined in lattice units
-    box = distances are defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
-change_box all x scale 1.1 y volume z volume remap 
-
    -

    Description: -

    -

    Change the volume and/or shape and/or boundary conditions for the -simulation box. Orthogonal simulation boxes have 3 adjustable size -parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have -6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of -them can be adjusted independently by this command. Thus it can be -used to expand or contract a box, or to apply a shear strain to a -non-orthogonal box. It can also be used to change the boundary -conditions for the simulation box, similar to the -boundary command. -

    -

    The size and shape of the initial simulation box are specified by the -create_box or read_data or -read_restart command used to setup the simulation. -The size and shape may be altered by subsequent runs, e.g. by use of -the fix npt or fix deform commands. -The create_box, read data, and -read_restart commands also determine whether the -simulation box is orthogonal or triclinic and their doc pages explain -the meaning of the xy,xz,yz tilt factors. -

    -

    See Section_howto 12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used -triclinic representations. -

    -

    The keywords used in this command are applied sequentially to the -simulation box and the atoms in it, in the order specified. -

    -

    Before the sequence of keywords are invoked, the current box -size/shape is stored, in case a remap keyword is used to map the -atom coordinates from a previously stored box size/shape to the -current one. -

    -

    After all the keywords have been processed, any shrink-wrap boundary -conditions are invoked (see the boundary command) -which may change simulation box boundaries, and atoms are migrated to -new owning processors. -

    -

    IMPORTANT_NOTE: This means that you cannot use the change_box command -to enlarge a shrink-wrapped box, e.g. to make room to insert more -atoms via the create_atoms command, because the -simulation box will be re-shrink-wrapped before the change_box command -completes. Instead you could do something like this, assuming the -simulation box is non-periodic and atoms extend from 0 to 20 in all -dimensions: -

    -
    change_box all x final -10 20
-create_atoms 1 single -5 5 5   # this will fail to insert an atom 
-
    -
    change_box all x final -10 20 boundary f s s
-create_atoms 1 single -5 5 5
-change_box boundary s s s      # this will work 
-
    -

    IMPORTANT NOTE: Unlike the earlier "displace_box" version of this -command, atom remapping is NOT performed by default. This command -allows remapping to be done in a more general way, exactly when you -specify it (zero or more times) in the sequence of transformations. -Thus if you do not use the remap keyword, atom coordinates will not -be changed even if the box size/shape changes. If a uniformly -strained state is desired, the remap keyword should be specified. -

    -

    IMPORTANT NOTE: It is possible to lose atoms with this command. -E.g. by changing the box without remapping the atoms, and having atoms -end up outside of non-periodic boundaries. It is also possible to -alter bonds between atoms straddling a boundary in bad ways. E.g. by -converting a boundary from periodic to non-periodic. It is also -possible when remapping atoms to put them (nearly) on top of each -other. E.g. by converting a boundary from non-periodic to periodic. -All of these will typically lead to bad dynamics and/or generate error -messages. -

    -

    IMPORTANT NOTE: The simulation box size/shape can be changed by -arbitrarily large amounts by this command. This is not a problem, -except that the mapping of processors to the simulation box is not -changed from its initial 3d configuration; see the -processors command. Thus, if the box size/shape -changes dramatically, the mapping of processors to the simulation box -may not end up as optimal as the initial mapping attempted to be. -

    -

    IMPORTANT NOTE: Because the keywords used in this command are applied -one at a time to the simulation box and the atoms in it, care must be -taken with triclinic cells to avoid exceeding the limits on skew after -each transformation in the sequence. If skew is exceeded before the -final transformation this can be avoided by changing the order of the -sequence, or breaking the transformation into two or more smaller -transformations. For more information on the allowed limits for box -skew see the discussion on triclinic boxes on this -page. -

    -
    - -

    For the x, y, and z parameters, this is the meaning of their -styles and values. -

    -

    For style final, the final lo and hi box boundaries of a dimension -are specified. The values can be in lattice or box distance units. -See the discussion of the units keyword below. -

    -

    For style delta, plus or minus changes in the lo/hi box boundaries -of a dimension are specified. The values can be in lattice or box -distance units. See the discussion of the units keyword below. -

    -

    For style scale, a multiplicative factor to apply to the box length -of a dimension is specified. For example, if the initial box length -is 10, and the factor is 1.1, then the final box length will be 11. A -factor less than 1.0 means compression. -

    -

    The volume style changes the specified dimension in such a way that -the overall box volume remains constant with respect to the operation -performed by the preceding keyword. The volume style can only be -used following a keyword that changed the volume, which is any of the -x, y, z keywords. If the preceding keyword "key" had a volume -style, then both it and the current keyword apply to the keyword -preceding "key". I.e. this sequence of keywords is allowed: -

    -
    change_box all x scale 1.1 y volume z volume 
-
    -

    The volume style changes the associated dimension so that the -overall box volume is unchanged relative to its value before the -preceding keyword was invoked. -

    -

    If the following command is used, then the z box length will shrink by -the same 1.1 factor the x box length was increased by: -

    -
    change_box all x scale 1.1 z volume 
-
    -

    If the following command is used, then the y,z box lengths will each -shrink by sqrt(1.1) to keep the volume constant. In this case, the -y,z box lengths shrink so as to keep their relative aspect ratio -constant: -

    -
    change_box all"x scale 1.1 y volume z volume 
-
    -

    If the following command is used, then the final box will be a factor -of 10% larger in x and y, and a factor of 21% smaller in z, so as to -keep the volume constant: -

    -
    change_box all x scale 1.1 z volume y scale 1.1 z volume 
-
    -

    IMPORTANT NOTE: For solids or liquids, when one dimension of the box -is expanded, it may be physically undesirable to hold the other 2 box -lengths constant since that implies a density change. For solids, -adjusting the other dimensions via the volume style may make -physical sense (just as for a liquid), but may not be correct for -materials and potentials whose Poisson ratio is not 0.5. -

    -

    For the scale and volume styles, the box length is expanded or -compressed around its mid point. -

    -
    - -

    For the xy, xz, and yz parameters, this is the meaning of their -styles and values. Note that changing the tilt factors of a triclinic -box does not change its volume. -

    -

    For style final, the final tilt factor is specified. The value -can be in lattice or box distance units. See the discussion of the -units keyword below. -

    -

    For style delta, a plus or minus change in the tilt factor is -specified. The value can be in lattice or box distance units. See -the discussion of the units keyword below. -

    -

    All of these styles change the xy, xz, yz tilt factors. In LAMMPS, -tilt factors (xy,xz,yz) for triclinic boxes are required to be no more -than half the distance of the parallel box length. For example, if -xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt -factor must be between -5 and 5. Similarly, both xz and yz must be -between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all equivalent. Any tilt factor specified by this command -must be within these limits. -

    -
    - -

    The boundary keyword takes arguments that have exactly the same -meaning as they do for the boundary command. In each -dimension, a single letter assigns the same style to both the lower -and upper face of the box. Two letters assigns the first style to the -lower face and the second style to the upper face. -

    -

    The style p means the box is periodic; the other styles mean -non-periodic. For style f, the position of the face is fixed. For -style s, the position of the face is set so as to encompass the -atoms in that dimension (shrink-wrapping), no matter how far they -move. For style m, shrink-wrapping occurs, but is bounded by the -current box edge in that dimension, so that the box will become no -smaller. See the boundary command for more -explanation of these style options. -

    -

    Note that the "boundary" command itself can only be used before the -simulation box is defined via a read_data or -create_box or read_restart -command. This command allows the boundary conditions to be changed -later in your input script. Also note that the -read_restart will change boundary conditions to -match what is stored in the restart file. So if you wish to change -them, you should use the change_box command after the read_restart -command. -

    -
    - -

    The ortho and triclinic keywords convert the simulation box to be -orthogonal or triclinic (non-orthongonal). See this -section for a discussion of how non-orthongal -boxes are represented in LAMMPS. -

    -

    The simulation box is defined as either orthogonal or triclinic when -it is created via the create_box, -read_data, or read_restart -commands. -

    -

    These keywords allow you to toggle the existing simulation box from -orthogonal to triclinic and vice versa. For example, an initial -equilibration simulation can be run in an orthogonal box, the box can -be toggled to triclinic, and then a non-equilibrium MD (NEMD) -simulation can be run with deformation -via the fix deform command. -

    -

    If the simulation box is currently triclinic and has non-zero tilt in -xy, yz, or xz, then it cannot be converted to an orthogonal box. -

    -
    - -

    The set keyword saves the current box size/shape. This can be -useful if you wish to use the remap keyword more than once or if you -wish it to be applied to an intermediate box size/shape in a sequence -of keyword operations. Note that the box size/shape is saved before -any of the keywords are processed, i.e. the box size/shape at the time -the create_box command is encountered in the input script. -

    -

    The remap keyword remaps atom coordinates from the last saved box -size/shape to the current box state. For example, if you stretch the -box in the x dimension or tilt it in the xy plane via the x and xy -keywords, then the remap commmand will dilate or tilt the atoms to -conform to the new box size/shape, as if the atoms moved with the box -as it deformed. -

    -

    Note that this operation is performed without regard to periodic -boundaries. Also, any shrink-wrapping of non-periodic boundaries (see -the boundary command) occurs after all keywords, -including this one, have been processed. -

    -

    Only atoms in the specified group are remapped. -

    -
    - -

    The units keyword determines the meaning of the distance units used -to define various arguments. A box value selects standard distance -units as defined by the units command, e.g. Angstroms for -units = real or metal. A lattice value means the distance units are -in lattice spacings. The lattice command must have -been previously used to define the lattice spacing. -

    -
    - -

    Restrictions: -

    -

    If you use the ortho or triclinic keywords, then at the point in -the input script when this command is issued, no dumps can -be active, nor can a fix ave/spatial or fix -deform be active. This is because these commands -test whether the simulation box is orthogonal when they are first -issued. Note that these commands can be used in your script before a -change_box command is issued, so long as an undump or -unfix command is also used to turn them off. -

    -

    Related commands: -

    -

    fix deform, boundary -

    -

    Default: -

    -

    The option default is units = lattice. -

    - diff --git a/doc/doc2/clear.html b/doc/doc2/clear.html deleted file mode 100644 index ddb7f19a13..0000000000 --- a/doc/doc2/clear.html +++ /dev/null @@ -1,43 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    clear command -

    -

    Syntax: -

    -
    clear 
-
    -

    Examples: -

    -
    (commands for 1st simulation)
-clear
-(commands for 2nd simulation) 
-
    -

    Description: -

    -

    This command deletes all atoms, restores all settings to their default -values, and frees all memory allocated by LAMMPS. Once a clear -command has been executed, it is almost as if LAMMPS were starting -over, with only the exceptions noted below. This command enables -multiple jobs to be run sequentially from one input script. -

    -

    These settings are not affected by a clear command: the working -directory (shell command), log file status -(log command), echo status (echo command), and -input script variables (variable command). -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/comm_modify.html b/doc/doc2/comm_modify.html deleted file mode 100644 index a11608a8fd..0000000000 --- a/doc/doc2/comm_modify.html +++ /dev/null @@ -1,167 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    comm_modify command -

    -

    Syntax: -

    -
    comm_modify keyword value ... 
-
    -
    • zero or more keyword/value pairs may be appended - -
    • keyword = mode or cutoff or cutoff/multi or group or vel - -
        mode value = single or multi = communicate atoms within a single or multiple distances
-  cutoff value = Rcut (distance units) = communicate atoms from this far away
-  cutoff/multi type value
-     type = atom type or type range (supports asterisk notation)
-     value = Rcut (distance units) = communicate atoms for selected types from this far away
-  group value = group-ID = only communicate atoms in the group
-  vel value = yes or no = do or do not communicate velocity info with ghost atoms 
-
      - -
    -

    Examples: -

    -
    comm_modify mode multi
-comm_modify mode multi group solvent
-comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
-comm_modify vel yes
-comm_modify mode single cutoff 5.0 vel yes
-comm_modify cutoff/multi * 0.0 
-
    -

    Description: -

    -

    This command sets parameters that affect the inter-processor -communication of atom information that occurs each timestep as -coordinates and other properties are exchanged between neighboring -processors and stored as properties of ghost atoms. -

    -

    IMPORTANT NOTE: These options apply to the currently defined comm -style. When you specify a comm_style command, all -communication settings are restored to their default values, including -those previously reset by a comm_modify command. Thus if your input -script specifies a comm_style command, you should use the comm_modify -command after it. -

    -

    The mode keyword determines whether a single or multiple cutoff -distances are used to determine which atoms to communicate. -

    -

    The default mode is single which means each processor acquires -information for ghost atoms that are within a single distance from its -sub-domain. The distance is by default the maximum of the neighbor -cutoff across all atom type pairs. -

    -

    For many systems this is an efficient algorithm, but for systems with -widely varying cutoffs for different type pairs, the multi mode can -be faster. In this case, each atom type is assigned its own distance -cutoff for communication purposes, and fewer atoms will be -communicated. See the neighbor multi command for a -neighbor list construction option that may also be beneficial for -simulations of this kind. -

    -

    The cutoff keyword allows you to extend the ghost cutoff distance -for communication mode single, which is the distance from the borders -of a processor's sub-domain at which ghost atoms are acquired from other -processors. By default the ghost cutoff = neighbor cutoff = pairwise -force cutoff + neighbor skin. See the neighbor command -for more information about the skin distance. If the specified Rcut is -greater than the neighbor cutoff, then extra ghost atoms will be acquired. -If the provided cutoff is smaller, the provided value will be ignored -and the ghost cutoff is set to the neighbor cutoff. Specifying a -cutoff value of 0.0 will reset any previous value to the default. -

    -

    The cutoff/multi option is equivalent to cutoff, but applies to -communication mode multi instead. Since in this case the communication -cutoffs are determined per atom type, a type specifier is needed and -cutoff for one or multiple types can be extended. Also ranges of types -using the usual asterisk notation can be given. -

    -

    These are simulation scenarios in which it may be useful or even -necessary to set a ghost cutoff > neighbor cutoff: -

    -
    • a single polymer chain with bond interactions, but no pairwise interactions -
    • bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff -
    • ghost atoms beyond the pairwise cutoff are needed for some computation -
    -

    In the first scenario, a pairwise potential is not defined. Thus the -pairwise neighbor cutoff will be 0.0. But ghost atoms are still -needed for computing bond, angle, etc interactions between atoms on -different processors, or when the interaction straddles a periodic -boundary. -

    -

    The appropriate ghost cutoff depends on the newton bond -setting. For newton bond off, the distance needs to be the furthest -distance between any two atoms in the bond, angle, etc. E.g. the -distance between 1-4 atoms in a dihedral. For newton bond on, the -distance between the central atom in the bond, angle, etc and any -other atom is sufficient. E.g. the distance between 2-4 atoms in a -dihedral. -

    -

    In the second scenario, a pairwise potential is defined, but its -neighbor cutoff is not sufficiently long enough to enable bond, angle, -etc terms to be computed. As in the previous scenario, an appropriate -ghost cutoff should be set. -

    -

    In the last scenario, a fix or compute or -pairwise potential needs to calculate with ghost -atoms beyond the normal pairwise cutoff for some computation it -performs (e.g. locate neighbors of ghost atoms in a multibody pair -potential). Setting the ghost cutoff appropriately can insure it will -find the needed atoms. -

    -

    IMPORTANT NOTE: In these scenarios, if you do not set the ghost cutoff -long enough, and if there is only one processor in a periodic -dimension (e.g. you are running in serial), then LAMMPS may "find" the -atom it is looking for (e.g. the partner atom in a bond), that is on -the far side of the simulation box, across a periodic boundary. This -will typically lead to bad dynamics (i.e. the bond length is now the -simulation box length). To detect if this is happening, see the -neigh_modify cluster command. -

    -

    The group keyword will limit communication to atoms in the specified -group. This can be useful for models where no ghost atoms are needed -for some kinds of particles. All atoms (not just those in the -specified group) will still migrate to new processors as they move. -The group specified with this option must also be specified via the -atom_modify first command. -

    -

    The vel keyword enables velocity information to be communicated with -ghost particles. Depending on the atom_style, -velocity info includes the translational velocity, angular velocity, -and angular momentum of a particle. If the vel option is set to -yes, then ghost atoms store these quantities; if no then they do -not. The yes setting is needed by some pair styles which require -the velocity state of both the I and J particles to compute a pairwise -I,J interaction. -

    -

    Note that if the fix deform command is being used -with its "remap v" option enabled, then the velocities for ghost atoms -(in the fix deform group) mirrored across a periodic boundary will -also include components due to any velocity shift that occurs across -that boundary (e.g. due to dilation or shear). -

    -

    Restrictions: -

    -

    Communication mode multi is currently only available for -comm_style brick. -

    -

    Related commands: -

    -

    comm_style, neighbor -

    -

    Default: -

    -

    The option defauls are mode = single, group = all, cutoff = 0.0, vel = -no. The cutoff default of 0.0 means that ghost cutoff = neighbor -cutoff = pairwise force cutoff + neighbor skin. -

    - diff --git a/doc/doc2/comm_style.html b/doc/doc2/comm_style.html deleted file mode 100644 index 9e4c23a7fb..0000000000 --- a/doc/doc2/comm_style.html +++ /dev/null @@ -1,68 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    comm_style command -

    -

    Syntax: -

    -
    comm_style style 
-
    -
    • style = brick or tiled -
    -

    Examples: -

    -
    comm_style brick
-comm_style tiled 
-
    -

    Description: -

    -

    This command sets the style of inter-processor communication of atom -information that occurs each timestep as coordinates and other -properties are exchanged between neighboring processors and stored as -properties of ghost atoms. -

    -

    For the default brick style, the domain decomposition used by LAMMPS -to partition the simulation box must be a regular 3d grid of bricks, -one per processor. Each processor communicates with its 6 Cartesian -neighbors in the grid to acquire information for nearby atoms. -

    -

    For the tiled style, a more general domain decomposition can be -used, as triggered by the balance or fix -balance commands. The simulation box can be -partitioned into non-overlapping rectangular-shaped "tiles" or varying -sizes and shapes. Again there is one tile per processor. To acquire -information for nearby atoms, communication must now be done with a -more complex pattern of neighboring processors. -

    -

    Note that this command does not actually define a partitoining of the -simulation box (a domain decomposition), rather it determines what -kinds of decompositions are allowed and the pattern of communication -used to enable the decomposition. A decomposition is created when the -simulation box is first created, via the create_box -or read_data or read_restart -commands. For both the brick and tiled styles, the initial -decomposition will be the same, as described by -create_box and processors -commands. The decomposition can be changed via the -balance or fix_balance commands. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    comm_modify, processors, -balance, fix balance -

    -

    Default: -

    -

    The default style is brick. -

    - diff --git a/doc/doc2/compute.html b/doc/doc2/compute.html deleted file mode 100644 index 0752ccf682..0000000000 --- a/doc/doc2/compute.html +++ /dev/null @@ -1,265 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute command -

    -

    Syntax: -

    -
    compute ID group-ID style args 
-
    -
    • ID = user-assigned name for the computation -
    • group-ID = ID of the group of atoms to perform the computation on -
    • style = one of a list of possible style names (see below) -
    • args = arguments used by a particular style -
    -

    Examples: -

    -
    compute 1 all temp
-compute newtemp flow temp/partial 1 1 0
-compute 3 all ke/atom 
-
    -

    Description: -

    -

    Define a computation that will be performed on a group of atoms. -Quantities calculated by a compute are instantaneous values, meaning -they are calculated from information about atoms on the current -timestep or iteration, though a compute may internally store some -information about a previous state of the system. Defining a compute -does not perform a computation. Instead computes are invoked by other -LAMMPS commands as needed, e.g. to calculate a temperature needed for -a thermostat fix or to generate thermodynamic or dump file output. -See this howto section for a summary of -various LAMMPS output options, many of which involve computes. -

    -

    The ID of a compute can only contain alphanumeric characters and -underscores. -

    -
    - -

    Computes calculate one of three styles of quantities: global, -per-atom, or local. A global quantity is one or more system-wide -values, e.g. the temperature of the system. A per-atom quantity is -one or more values per atom, e.g. the kinetic energy of each atom. -Per-atom values are set to 0.0 for atoms not in the specified compute -group. Local quantities are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. Computes that produce per-atom quantities have the -word "atom" in their style, e.g. ke/atom. Computes that produce -local quantities have the word "local" in their style, -e.g. bond/local. Styles with neither "atom" or "local" in their -style produce global quantities. -

    -

    Note that a single compute produces either global or per-atom or local -quantities, but never more than one of these. -

    -

    Global, per-atom, and local quantities each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for each compute describes the style and kind of values it -produces, e.g. a per-atom vector. Some computes produce more than one -kind of a single style, e.g. a global scalar and a global vector. -

    -

    When a compute quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID is the ID of the compute: -

    -
    - - -
    c_ID entire scalar, vector, or array
    c_ID[I] one element of vector, one column of array
    c_ID[I][J] one element of array -
    - -

    In other words, using one bracket reduces the dimension of the -quantity once (vector -> scalar, array -> vector). Using two brackets -reduces the dimension twice (array -> scalar). Thus a command that -uses scalar compute values as input can also process elements of a -vector or array. -

    -

    Note that commands and variables which use compute -quantities typically do not allow for all kinds, e.g. a command may -require a vector of values, not a scalar. This means there is no -ambiguity about referring to a compute quantity as c_ID even if it -produces, for example, both a scalar and vector. The doc pages for -various commands explain the details. -

    -
    - -

    In LAMMPS, the values generated by a compute can be used in several -ways: -

    - -

    The results of computes that calculate global quantities can be either -"intensive" or "extensive" values. Intensive means the value is -independent of the number of atoms in the simulation, -e.g. temperature. Extensive means the value scales with the number of -atoms in the simulation, e.g. total rotational kinetic energy. -Thermodynamic output will normalize extensive -values by the number of atoms in the system, depending on the -"thermo_modify norm" setting. It will not normalize intensive values. -If a compute value is accessed in another way, e.g. by a -variable, you may want to know whether it is an -intensive or extensive value. See the doc page for individual -computes for further info. -

    -
    - -

    LAMMPS creates its own computes internally for thermodynamic output. -Three computes are always created, named "thermo_temp", -"thermo_press", and "thermo_pe", as if these commands had been invoked -in the input script: -

    -
    compute thermo_temp all temp
-compute thermo_press all pressure thermo_temp
-compute thermo_pe all pe 
-
    -

    Additional computes for other quantities are created if the thermo -style requires it. See the documentation for the -thermo_style command. -

    -

    Fixes that calculate temperature or pressure, i.e. for thermostatting -or barostatting, may also create computes. These are discussed in the -documentation for specific fix commands. -

    -

    In all these cases, the default computes LAMMPS creates can be -replaced by computes defined by the user in the input script, as -described by the thermo_modify and fix -modify commands. -

    -

    Properties of either a default or user-defined compute can be modified -via the compute_modify command. -

    -

    Computes can be deleted with the uncompute command. -

    -

    Code for new computes can be added to LAMMPS (see this -section of the manual) and the results of their -calculations accessed in the various ways described above. -

    -
    - -

    Each compute style has its own doc page which describes its arguments -and what it does. Here is an alphabetic list of compute styles -available in LAMMPS. They are also given in more compact form in the -Compute section of this page. -

    -

    There are also additional compute styles (not listed here) submitted -by users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the compute -section of this page. -

    -
    • angle/local - theta and energy of each angle -
    • angmom/chunk - angular momentum for each chunk -
    • body/local - attributes of body sub-particles -
    • bond/local - distance and energy of each bond -
    • centro/atom - centro-symmetry parameter for each atom -
    • chunk/atom - assign chunk IDs to each atom -
    • cluster/atom - cluster ID for each atom -
    • cna/atom - common neighbor analysis (CNA) for each atom -
    • com - center-of-mass of group of atoms -
    • com/chunk - center-of-mass for each chunk -
    • contact/atom - contact count for each spherical particle -
    • coord/atom - coordination number for each atom -
    • damage/atom - Peridynamic damage for each atom -
    • dihedral/local - angle of each dihedral -
    • dilatation/atom - Peridynamic dilatation for each atom -
    • displace/atom - displacement of each atom -
    • erotate/asphere - rotational energy of aspherical particles -
    • erotate/rigid - rotational energy of rigid bodies -
    • erotate/sphere - rotational energy of spherical particles -
    • erotate/sphere/atom - rotational energy for each spherical particle -
    • event/displace - detect event on atom displacement -
    • group/group - energy/force between two groups of atoms -
    • gyration - radius of gyration of group of atoms -
    • gyration/chunk - radius of gyration for each chunk -
    • heat/flux - heat flux through a group of atoms -
    • hexorder/atom - bond orientational order parameter q6 -
    • improper/local - angle of each improper -
    • inertia/chunk - inertia tensor for each chunk -
    • ke - translational kinetic energy -
    • ke/atom - kinetic energy for each atom -
    • ke/rigid - translational kinetic energy of rigid bodies -
    • msd - mean-squared displacement of group of atoms -
    • msd/chunk - mean-squared displacement for each chunk -
    • msd/nongauss - MSD and non-Gaussian parameter of group of atoms -
    • omega/chunk - angular velocity for each chunk -
    • orientorder/atom - Steinhardt bond orientational order parameters Ql -
    • pair - values computed by a pair style -
    • pair/local - distance/energy/force of each pairwise interaction -
    • pe - potential energy -
    • pe/atom - potential energy for each atom -
    • plasticity/atom - Peridynamic plasticity for each atom -
    • pressure - total pressure and pressure tensor -
    • property/atom - convert atom attributes to per-atom vectors/arrays -
    • property/local - convert local attributes to localvectors/arrays -
    • property/chunk - extract various per-chunk attributes -
    • rdf - radial distribution function g(r) histogram of group of atoms -
    • reduce - combine per-atom quantities into a single global value -
    • reduce/region - same as compute reduce, within a region -
    • slice - extract values from global vector or array -
    • sna/atom - calculate bispectrum coefficients for each atom -
    • snad/atom - derivative of bispectrum coefficients for each atom -
    • snav/atom - virial contribution from bispectrum coefficients for each atom -
    • stress/atom - stress tensor for each atom -
    • temp - temperature of group of atoms -
    • temp/asphere - temperature of aspherical particles -
    • temp/chunk - temperature of each chunk -
    • temp/com - temperature after subtracting center-of-mass velocity -
    • temp/deform - temperature excluding box deformation velocity -
    • temp/partial - temperature excluding one or more dimensions of velocity -
    • temp/profile - temperature excluding a binned velocity profile -
    • temp/ramp - temperature excluding ramped velocity component -
    • temp/region - temperature of a region of atoms -
    • temp/sphere - temperature of spherical particles -
    • ti - thermodyanmic integration free energy values -
    • torque/chunk - torque applied on each chunk -
    • vacf - velocity-autocorrelation function of group of atoms -
    • vcm/chunk - velocity of center-of-mass for each chunk -
    • voronoi/atom - Voronoi volume and neighbors for each atom -
    -

    There are also additional compute styles submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the compute section of this -page. -

    -

    There are also additional accelerated compute styles included in the -LAMMPS distribution for faster performance on CPUs and GPUs. The list -of these with links to the individual styles are given in the pair -section of this page. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    uncompute, compute_modify, fix -ave/atom, fix ave/spatial, -fix ave/time, fix ave/histo -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_ackland_atom.html b/doc/doc2/compute_ackland_atom.html deleted file mode 100644 index d3445f2f52..0000000000 --- a/doc/doc2/compute_ackland_atom.html +++ /dev/null @@ -1,80 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute ackland/atom command -

    -

    Syntax: -

    -
    compute ID group-ID ackland/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • ackland/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all ackland/atom 
-
    -

    Description: -

    -

    Defines a computation that calculates the local lattice structure -according to the formulation given in (Ackland). -

    -

    In contrast to the centro-symmetry -parameter this method is stable against -temperature boost, because it is based not on the distance between -particles but the angles. Therefore statistical fluctuations are -averaged out a little more. A comparison with the Common Neighbor -Analysis metric is made in the paper. -

    -

    The result is a number which is mapped to the following different -lattice structures: -

    -
    • 0 = UNKNOWN -
    • 1 = BCC -
    • 2 = FCC -
    • 3 = HCP -
    • 4 = ICO -
    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each of -which computes this quantity.- -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    Restrictions: -

    -

    This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    The per-atom vector values will be unitless since they are the -integers defined above. -

    -

    Related commands: -

    -

    compute centro/atom -

    -

    Default: none -

    -
    - - - -

    (Ackland) Ackland, Jones, Phys Rev B, 73, 054104 (2006). -

    - diff --git a/doc/doc2/compute_angle_local.html b/doc/doc2/compute_angle_local.html deleted file mode 100644 index 60ba03541f..0000000000 --- a/doc/doc2/compute_angle_local.html +++ /dev/null @@ -1,87 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute angle/local command -

    -

    Syntax: -

    -
    compute ID group-ID angle/local input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • angle/local = style name of this compute command - -
    • one or more keywords may be appended - -
    • keyword = theta or eng - -
        theta = tabulate angles
-  eng = tabulate angle energies 
-
      - -
    -

    Examples: -

    -
    compute 1 all angle/local theta
-compute 1 all angle/local eng theta 
-
    -

    Description: -

    -

    Define a computation that calculates properties of individual angle -interactions. The number of datums generated, aggregated across all -processors, equals the number of angles in the system, modified by the -group parameter as explained below. -

    -

    The local data stored by this command is generated by looping over all -the atoms owned on a processor and their angles. An angle will only -be included if all 3 atoms in the angle are in the specified compute -group. Any angles that have been broken (see the -angle_style command) by setting their angle type to -0 are not included. Angles that have been turned off (see the fix -shake or delete_bonds commands) by -setting their angle type negative are written into the file, but their -energy will be 0.0. -

    -

    Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, angle output from the compute -property/local command can be combined -with data from this command and output by the dump local -command in a consistent way. -

    -

    Output info: -

    -

    This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of angles. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The output for theta will be in degrees. The output for eng will -be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump local, compute -property/local -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_angmom_chunk.html b/doc/doc2/compute_angmom_chunk.html deleted file mode 100644 index 2017422f12..0000000000 --- a/doc/doc2/compute_angmom_chunk.html +++ /dev/null @@ -1,94 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute angmom/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID angmom/chunk chunkID 
-
    -
    • ID, group-ID are documented in compute command -
    • angmom/chunk = style name of this compute command -
    • chunkID = ID of compute chunk/atom command -
    -

    Examples: -

    -
    compute 1 fluid angmom/chunk molchunk 
-
    -

    Description: -

    -

    Define a computation that calculates the angular momemtum of multiple -chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates the 3 components of the angular momentum -vector for each chunk, due to the velocity/momentum of the individual -atoms in the chunk around the center-of-mass of the chunk. The -calculation includes all effects due to atoms passing thru periodic -boundaries. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's -angular momentum in "unwrapped" form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    The simplest way to output the results of the compute angmom/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all angmom/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array where the number of rows = the -number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The number of columns = -3 for the 3 xyz components of the angular momentum for each chunk. -These values can be accessed by any command that uses global array -values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The array values are "intensive". The array values will be in -mass-velocity-distance units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    variable angmom() function -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_basal_atom.html b/doc/doc2/compute_basal_atom.html deleted file mode 100644 index 8427c4e4fa..0000000000 --- a/doc/doc2/compute_basal_atom.html +++ /dev/null @@ -1,82 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute basal/atom command -

    -

    Syntax: -

    -
    compute ID group-ID basal/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • basal/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all basal/atom 
-
    -

    Description: -

    -

    Defines a computation that calculates the hexagonal close-packed "c" -lattice vector for each atom in the group. It does this by -calculating the normal unit vector to the basal plane for each atom. -The results enable efficient identification and characterization of -twins and grains in hexagonal close-packed structures. -

    -

    The output of the compute is thus the 3 components of a unit vector -associdate with each atom. The components are set to 0.0 for -atoms not in the group. -

    -

    Details of the calculation are given in (Barrett). -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each of -which computes this quantity. -

    -

    An example input script that uses this compute is provided -in examples/USER/misc/basal. -

    -

    Output info: -

    -

    This compute calculates a per-atom array with 3 columns, which can be -accessed by indices 1-3 by any command that uses per-atom values from -a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The per-atom vector values are unitless since the 3 columns represent -components of a unit vector. -

    -

    Restrictions: -

    -

    This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    The output of this compute will be meaningless unless the atoms are on -(or near) hcp lattice sites, since the calculation assumes a -well-defined basal plane. -

    -

    Related commands: -

    -

    compute centro/atom, compute -ackland/atom -

    -

    Default: none -

    -
    - - - -

    (Barrett) Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012). -

    - diff --git a/doc/doc2/compute_body_local.html b/doc/doc2/compute_body_local.html deleted file mode 100644 index 7b8b74dfea..0000000000 --- a/doc/doc2/compute_body_local.html +++ /dev/null @@ -1,99 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute body/local command -

    -

    Syntax: -

    -
    compute ID group-ID body/local input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • body/local = style name of this compute command - -
    • one or more keywords may be appended - -
    • keyword = type or integer - -
        type = atom type of the body particle
-  integer = 1,2,3,etc = index of fields defined by body style 
-
      - -
    -

    Examples: -

    -
    compute 1 all body/local type 1 2 3
-compute 1 all body/local 3 6 
-
    -

    Description: -

    -

    Define a computation that calculates properties of individual body -sub-particles. The number of datums generated, aggregated across all -processors, equals the number of body sub-particles plus the number of -non-body particles in the system, modified by the group parameter as -explained below. See Section_howto 14 -of the manual and the body doc page for more details on -using body particles. -

    -

    The local data stored by this command is generated by looping over all -the atoms. An atom will only be included if it is in the group. If -the atom is a body particle, then its N sub-particles will be looped -over, and it will contribute N datums to the count of datums. If it -is not a body particle, it will contribute 1 datum. -

    -

    For both body particles and non-body particles, the type keyword -will store the type of the atom. -

    -

    The integer keywords mean different things for body and non-body -particles. If the atom is not a body particle, only its x, y, z -coordinates can be referenced, using the integer keywords 1,2,3. -Note that this means that if you want to access more fields than this -for body particles, then you cannot include non-body particles in the -group. -

    -

    For a body particle, the integer keywords refer to fields calculated -by the body style for each sub-particle. The body style, as specified -by the atom_style body, determines how many fields -exist and what they are. See the body doc page for -details of the different styles. -

    -

    Here is an example of how to output body information using the dump -local command with this compute. If fields 1,2,3 for the -body sub-particles are x,y,z coordinates, then the dump file will be -formatted similar to the output of a dump atom or custom -command. -

    -
    compute 1 all body/local type 1 2 3
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] 
-
    -

    Output info: -

    -

    This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of datums as described above. If a single keyword -is specified, a local vector is produced. If two or more keywords are -specified, a local array is produced where the number of columns = the -number of keywords. The vector or array can be accessed by any -command that uses local values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The units for output values depend on the body style. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump local -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_bond_local.html b/doc/doc2/compute_bond_local.html deleted file mode 100644 index db281b4fa7..0000000000 --- a/doc/doc2/compute_bond_local.html +++ /dev/null @@ -1,94 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute bond/local command -

    -

    Syntax: -

    -
    compute ID group-ID bond/local input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • bond/local = style name of this compute command - -
    • one or more keywords may be appended - -
    • keyword = dist or eng - -
        dist = bond distance
-  eng = bond energy
-  force = bond force 
-
      - -
    -

    Examples: -

    -
    compute 1 all bond/local eng
-compute 1 all bond/local dist eng force 
-
    -

    Description: -

    -

    Define a computation that calculates properties of individual bond -interactions. The number of datums generated, aggregated across all -processors, equals the number of bonds in the system, modified -by the group parameter as explained below. -

    -

    The local data stored by this command is generated by looping over all -the atoms owned on a processor and their bonds. A bond will only be -included if both atoms in the bond are in the specified compute group. -Any bonds that have been broken (see the bond_style -command) by setting their bond type to 0 are not included. Bonds that -have been turned off (see the fix shake or -delete_bonds commands) by setting their bond type -negative are written into the file, but their energy will be 0.0. -

    -

    Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, bond output from the compute -property/local command can be combined -with data from this command and output by the dump local -command in a consistent way. -

    -

    Here is an example of how to do this: -

    -
    compute 1 all property/local batom1 batom2 btype 
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] 
-
    -

    Output info: -

    -

    This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of bonds. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The output for dist will be in distance units. The -output for eng will be in energy units. The output for -force will be in force units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump local, compute -property/local -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_centro_atom.html b/doc/doc2/compute_centro_atom.html deleted file mode 100644 index 6b3c037103..0000000000 --- a/doc/doc2/compute_centro_atom.html +++ /dev/null @@ -1,126 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute centro/atom command -

    -

    Syntax: -

    -
    compute ID group-ID centro/atom lattice 
-
    -
    • ID, group-ID are documented in compute command -
    • centro/atom = style name of this compute command -
    • lattice = fcc or bcc or N = # of neighbors per atom to include -
    -

    Examples: -

    -
    compute 1 all centro/atom fcc 
-
    -
    compute 1 all centro/atom 8 
-
    -

    Description: -

    -

    Define a computation that calculates the centro-symmetry parameter for -each atom in the group. In solid-state systems the centro-symmetry -parameter is a useful measure of the local lattice disorder around an -atom and can be used to characterize whether the atom is part of a -perfect lattice, a local defect (e.g. a dislocation or stacking -fault), or at a surface. -

    -

    The value of the centro-symmetry parameter will be 0.0 for atoms not -in the specified compute group. -

    -

    This parameter is computed using the following formula from -(Kelchner) -

    -
    -
    -

    where the N nearest neighbors or each atom are identified and Ri and -Ri+N/2 are vectors from the central atom to a particular pair of -nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that -can contribute to this formula. The quantity in the sum is computed -for each, and the N/2 smallest are used. This will typically be for -pairs of atoms in symmetrically opposite positions with respect to the -central atom; hence the i+N/2 notation. -

    -

    N is an input parameter, which should be set to correspond to the -number of nearest neighbors in the underlying lattice of atoms. If -the keyword fcc or bcc is used, N is set to 12 and 8 -respectively. More generally, N can be set to a positive, even -integer. -

    -

    For an atom on a lattice site, surrounded by atoms on a perfect -lattice, the centro-symmetry parameter will be 0. It will be near 0 -for small thermal perturbations of a perfect lattice. If a point -defect exists, the symmetry is broken, and the parameter will be a -larger positive value. An atom at a surface will have a large -positive parameter. If the atom does not have N neighbors (within -the potential cutoff), then its centro-symmetry parameter is set to -0.0. -

    -

    Only atoms within the cutoff of the pairwise neighbor list are -considered as possible neighbors. Atoms not in the compute group are -included in the N neighbors used in this calculation. -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (e.g. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each with a -centro/atom style. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values are unitless values >= 0.0. Their -magnitude depends on the lattice style due to the number of -contibuting neighbor pairs in the summation in the formula above. And -it depends on the local defects surrounding the central atom, as -described above. -

    -

    Here are typical centro-symmetry values, from a a nanoindentation -simulation into gold (FCC). These were provided by Jon Zimmerman -(Sandia): -

    -
    Bulk lattice = 0
-Dislocation core ~ 1.0 (0.5 to 1.25)
-Stacking faults ~ 5.0 (4.0 to 6.0)
-Free surface ~ 23.0 
-
    -

    These values are *not* normalized by the square of the lattice -parameter. If they were, normalized values would be: -

    -
    Bulk lattice = 0
-Dislocation core ~ 0.06 (0.03 to 0.075)
-Stacking faults ~ 0.3 (0.24 to 0.36)
-Free surface ~ 1.38 
-
    -

    For BCC materials, the values for dislocation cores and free surfaces -would be somewhat different, due to their being only 8 neighbors instead -of 12. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute cna/atom -

    -

    Default: none -

    -
    - - - -

    (Kelchner) Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998). -

    - diff --git a/doc/doc2/compute_chunk_atom.html b/doc/doc2/compute_chunk_atom.html deleted file mode 100644 index 24d4598c62..0000000000 --- a/doc/doc2/compute_chunk_atom.html +++ /dev/null @@ -1,568 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute chunk/atom command -

    -

    Syntax: -

    -
    compute ID group-ID chunk/atom style args keyword values ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • chunk/atom = style name of this compute command - -
      style = bin/1d or bin/2d or bin/3d or type or molecule or compute/fix/variable
-  bin/1d args = dim origin delta
-    dim = x or y or z
-    origin = lower or center or upper or coordinate value (distance units)
-    delta = thickness of spatial bins in dim (distance units)
-  bin/2d args = dim origin delta dim origin delta
-    dim = x or y or z
-    origin = lower or center or upper or coordinate value (distance units)
-    delta = thickness of spatial bins in dim (distance units)
-  bin/3d args = dim origin delta dim origin delta dim origin delta
-    dim = x or y or z
-    origin = lower or center or upper or coordinate value (distance units)
-    delta = thickness of spatial bins in dim (distance units)
-  type args = none
-  molecule args = none
-  compute/fix/variable = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args
-    c_ID = per-atom vector calculated by a compute with ID
-    c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-    f_ID = per-atom vector calculated by a fix with ID
-    f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-    v_name = per-atom vector calculated by an atom-style variable with name 
-
      -
    • zero or more keyword/values pairs may be appended - -
    • keyword = region or nchunk or static or compress or bound or discard or units - -
        region value = region-ID
-    region-ID = ID of region atoms must be in to be part of a chunk
-  nchunk value = once or every
-    once = only compute the number of chunks once
-    every = re-compute the number of chunks whenever invoked
-  limit values = 0 or Nc max or Nc exact
-    0 = no limit on the number of chunks
-    Nc max = limit number of chunks to be <= Nc
-    Nc exact = set number of chunks to exactly Nc
-  ids value = once or nfreq or every
-    once = assign chunk IDs to atoms only once, they persist thereafter
-    nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by fix ave/chunk which sets Nfreq)
-    every = assign chunk IDs to atoms whenever invoked
-  compress value = yes or no
-    yes = compress chunk IDs to eliminate IDs with no atoms
-    no = do not compress chunk IDs even if some IDs have no atoms
-  discard value = yes or no or mixed
-    yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
-    no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
-    mixed = keep or discard such atoms according to spatial binning rule
-  bound values = x/y/z lo hi
-    x/y/z = x or y or z to bound sptial bins in this dimension
-    lo = lower or coordinate value (distance units)
-    hi = upper or coordinate value (distance units)
-  units value = box or lattice or reduced 
-
      - -
    -

    Examples: -

    -
    compute 1 all chunk/atom type
-compute 1 all chunk/atom bin/1d z lower 0.02 units reduced
-compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5
-compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes 
-
    -

    Description: -

    -

    Define a computation that calculates an integer chunk ID from 1 to -Nchunk for each atom in the group. Values of chunk IDs are determined -by the style of chunk, which can be based on atom type or molecule -ID or spatial binning or a per-atom property or value calculated by -another compute, fix, or atom-style -variable. Per-atom chunk IDs can be used by other -computes with "chunk" in their style name, such as compute -com/chunk or compute -msd/chunk. Or they can be used by the fix -ave/chunk command to sum and time average a -variety of per-atom properties over the atoms in each chunk. Or they -can simply be accessed by any command that uses per-atom values from a -compute as input, as discussed in Section_howto -15. -

    -

    See Section_howto 23 for an overview of -how this compute can be used with a variety of other commands to -tabulate properties of a simulation. The howto section gives several -examples of input script commands that can be used to calculate -interesting properties. -

    -

    Conceptually it is important to realize that this compute does two -simple things. First, it sets the value of Nchunk = the number of -chunks, which can be a constant value or change over time. Second, it -assigns each atom to a chunk via a chunk ID. Chunk IDs range from 1 -to Nchunk inclusive; some chunks may have no atoms assigned to them. -Atoms that do not belong to any chunk are assigned a value of 0. Note -that the two operations are not always performed together. For -example, spatial bins can be setup once (which sets Nchunk), and -atoms assigned to those bins many times thereafter (setting their -chunk IDs). -

    -

    All other commands in LAMMPS that use chunk IDs assume there are -Nchunk number of chunks, and that every atom is assigned to one of -those chunks, or not assigned to any chunk. -

    -

    There are many options for specifying for how and when Nchunk is -calculated, and how and when chunk IDs are assigned to atoms. The -details depend on the chunk style and its args, as well as -optional keyword settings. They can also depend on whether a fix -ave/chunk command is using this compute, since -that command requires Nchunk to remain static across windows of -timesteps it specifies, while it accumulates per-chunk averages. -

    -

    The details are described below. -

    -
    - -
    - -

    The different chunk styles operate as follows. For each style, how it -calculates Nchunk and assigns chunk IDs to atoms is explained. Note -that using the optional keywords can change both of those actions, as -described further below where the keywords are discussed. -

    -
    - -

    The binning styles perform a spatial binning of atoms, and assign an -atom the chunk ID corresponding to the bin number it is in. Nchunk -is set to the number of bins, which can change if the simulation box -size changes. -

    -

    The bin/1d, bin/2d, and bin/3d styles define bins as 1d layers -(slabs), 2d pencils, or 3d boxes. The dim, origin, and delta -settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is -no restriction on specifying dim = x before dim = y or z, or dim = y -before dim = z. Bins in a particular dim have a bin size in that -dimension given by delta. In each dimension, bins are defined -relative to a specified origin, which may be the lower/upper edge of -the simulation box (in that dimension), or its center point, or a -specified coordinate value. Starting at the origin, sufficient bins -are created in both directions to completely span the simulation box -or the bounds specified by the optional bounds keyword. -

    -

    For orthogonal simulation boxes, the bins are layers, pencils, or -boxes aligned with the xyz coordinate axes. For triclinic -(non-orthogonal) simulation boxes, the bin faces are parallel to the -tilted faces of the simulation box. See this -section of the manual for a discussion of -the geometry of triclinic boxes in LAMMPS. As described there, a -tilted simulation box has edge vectors a,b,c. In that nomenclature, -bins in the x dimension have faces with normals in the "b" cross "c" -direction. Bins in y have faces normal to the "a" cross "c" -direction. And bins in z have faces normal to the "a" cross "b" -direction. Note that in order to define the size and position of -these bins in an unambiguous fashion, the units option must be set -to reduced when using a triclinic simulation box, as noted below. -

    -

    The meaning of origin and delta for triclinic boxes is as follows. -Consider a triclinic box with bins that are 1d layers or slabs in the -x dimension. No matter how the box is tilted, an origin of 0.0 -means start layers at the lower "b" cross "c" plane of the simulation -box and an origin of 1.0 means to start layers at the upper "b" -cross "c" face of the box. A delta value of 0.1 in reduced units -means there will be 10 layers from 0.0 to 1.0, regardless of the -current size or shape of the simulation box. -

    -

    The created bins (and hence the chunk IDs) are numbered consecutively -from 1 to the number of bins = Nchunk. For 2d and 3d bins, the -numbering varies most rapidly in the first dimension (which could be -x, y, or z), next rapidly in the 2nd dimension, and most slowly in the -3rd dimension. -

    -

    Each time this compute is invoked, each atom is mapped to a bin based -on its current position. Note that between reneighboring timesteps, -atoms can move outside the current simulation box. If the box is -periodic (in that dimension) the atom is remapping into the periodic -box for purposes of binning. If the box in not periodic, the atom may -have moved outside the bounds of all bins. If an atom is not inside -any bin, the discard keyword is used to determine how a chunk ID is -assigned to the atom. -

    -
    - -

    The type style uses the atom type as the chunk ID. Nchunk is set -to the number of atom types defined for the simulation, e.g. via the -create_box or read_data commands. -

    -
    - -

    The molecule style uses the molecule ID of each atom as its chunk -ID. Nchunk is set to the largest chunk ID. Note that this excludes -molecule IDs for atoms which are not in the specified group or -optional region. -

    -

    There is no requirement that all atoms in a particular molecule are -assigned the same chunk ID (zero or non-zero), though you probably -want that to be the case, if you wish to compute a per-molecule -property. LAMMPS will issue a warning if that is not the case, but -only the first time that Nchunk is calculated. -

    -

    Note that atoms with a molecule ID = 0, which may be non-molecular -solvent atoms, have an out-of-range chunk ID. These atoms are -discarded (not assigned to any chunk) or assigned to Nchunk, -depending on the value of the discard keyword. -

    -
    - -

    The compute/fix/variable styles set the chunk ID of each atom based -on a quantity calculated and stored by a compute, fix, or variable. -In each case, it must be a per-atom quantity. In each case the -referenced floating point values are converted to an integer chunk ID -as follows. The floating point value is truncated (rounded down) to -an integer value. If the integer value is <= 0, then a chunk ID of 0 -is assigned to the atom. If the integer value is > 0, it becomes the -chunk ID to the atom. Nchunk is set to the largest chunk ID. Note -that this excludes atoms which are not in the specified group or -optional region. -

    -

    If the style begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and add them to LAMMPS. -

    -

    If the style begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with the -timestep on which this compute accesses the fix, else an error -results. Users can also write code for their own fix styles and add -them to LAMMPS. -

    -

    If a value begins with "v_", a variable name for an atom or -atomfile style variable must follow which has been -previously defined in the input script. Variables of style atom can -reference thermodynamic keywords and various per-atom attributes, or -invoke other computes, fixes, or variables when they are evaluated, so -this is a very general means of generating per-atom quantities to -treat as a chunk ID. -

    -
    - -
    - -

    Normally, Nchunk = the number of chunks, is re-calculated every time -this fix is invoked, though the value may or may not change. As -explained below, the nchunk keyword can be set to once which means -Nchunk will never change. -

    -

    If a fix ave/chunk command uses this compute, it -can also turn off the re-calculation of Nchunk for one or more -windows of timesteps. The extent of the windows, during which Nchunk -is held constant, are determined by the Nevery, Nrepeat, Nfreq -values and the ave keyword setting that are used by the fix -ave/chunk command. -

    -

    Specifically, if ave = one, then for each span of Nfreq -timesteps, Nchunk is held constant between the first timestep when -averaging is done (within the Nfreq-length window), and the last -timestep when averaging is done (multiple of Nfreq). If ave = -running or window, then Nchunk is held constant forever, -starting on the first timestep when the fix -ave/chunk command invokes this compute. -

    -

    Note that multiple fix ave/chunk commands can use -the same compute chunk/atom compute. However, the time windows they -induce for holding Nchunk constant must be identical, else an error -will be generated. -

    -
    - -
    - -

    The various optional keywords operate as follows. Note that some of -them function differently or are ignored by different chunk styles. -Some of them also have different default values, depending on -the chunk style, as listed below. -

    -

    The region keyword applies to all chunk styles. If used, an atom -must be in both the specified group and the specified geometric -region to be assigned to a chunk. -

    -
    - -

    The nchunk keyword applies to all chunk styles. It specifies how -often Nchunk is recalculated, which in turn can affect the chunk IDs -assigned to individual atoms. -

    -

    If nchunk is set to once, then Nchunk is only calculated once, -the first time this compute is invoked. If nchunk is set to -every, then Nchunk is re-calculated every time the compute is -invoked. Note that, as described above, the use of this compute -by the fix ave/chunk command can override -the every setting. -

    -

    The default values for nchunk are listed below and depend on the -chunk style and other system and keyword settings. They attempt to -represent typical use cases for the various chunk styles. The -nchunk value can always be set explicitly if desired. -

    -
    - -

    The limit keyword can be used to limit the calculated value of -Nchunk = the number of chunks. The limit is applied each time -Nchunk is calculated, which also limits the chunk IDs assigned to -any atom. The limit keyword is used by all chunk styles except the -binning styles, which ignore it. This is because the number of bins -can be tailored using the bound keyword (described below) which -effectively limits the size of Nchunk. -

    -

    If limit is set to Nc = 0, then no limit is imposed on Nchunk, -though the compress keyword can still be used to reduce Nchunk, as -described below. -

    -

    If Nc > 0, then the effect of the limit keyword depends on whether -the compress keyword is also used with a setting of yes, and -whether the compress keyword is specified before the limit keyword -or after. -

    -

    In all cases, Nchunk is first calculated in the usual way for each -chunk style, as described above. -

    -

    First, here is what occurs if compress yes is not set. If limit -is set to Nc max, then Nchunk is reset to the smaller of Nchunk -and Nc. If limit is set to Nc exact, then Nchunk is reset to -Nc, whether the original Nchunk was larger or smaller than Nc. -If Nchunk shrank due to the limit setting, then atom chunk IDs > -Nchunk will be reset to 0 or Nchunk, depending on the setting of -the discard keyword. If Nchunk grew, there will simply be some -chunks with no atoms assigned to them. -

    -

    If compress yes is set, and the compress keyword comes before the -limit keyword, the compression operation is performed first, as -described below, which resets Nchunk. The limit keyword is then -applied to the new Nchunk value, exactly as described in the -preceeding paragraph. Note that in this case, all atoms will end up -with chunk IDs <= Nc, but their original values (e.g. molecule ID or -compute/fix/variable value) may have been > Nc, because of the -compression operation. -

    -

    If compress yes is set, and the compress keyword comes after the -limit keyword, then the limit value of Nc is applied first to -the uncompressed value of Nchunk, but only if Nc < Nchunk -(whether Nc max or Nc exact is used). This effectively means all -atoms with chunk IDs > Nc have their chunk IDs reset to 0 or Nc, -depending on the setting of the discard keyword. The compression -operation is then performed, which may shrink Nchunk further. If -the new Nchunk < Nc and limit = Nc exact is specified, then -Nchunk is reset to Nc, which results in extra chunks with no atoms -assigned to them. Note that in this case, all atoms will end up with -chunk IDs <= Nc, and their original values (e.g. molecule ID or -compute/fix/variable value) will also have been <= Nc. -

    -
    - -

    The ids keyword applies to all chunk styles. If the setting is -once then the chunk IDs assigned to atoms the first time this -compute is invoked will be permanent, and never be re-computed. -

    -

    If the setting is nfreq and if a fix ave/chunk -command is using this compute, then in each of the Nchunk = constant -time windows (discussed above), the chunk ID's assigned to atoms on -the first step of the time window will persist until the end of the -time window. -

    -

    If the setting is every, which is the default, then chunk IDs are -re-calculated on any timestep this compute is invoked. -

    -

    IMPORTANT NOTE: If you want the persistent chunk-IDs calculated by -this compute to be continuous when running from a restart -file, then you should use the same ID for this -compute, as in the original run. This is so that the fix this compute -creates to store per-atom quantities will also have the same ID, and -thus be initialized correctly with chunk IDs from the restart file. -

    -
    - -

    The compress keyword applies to all chunk styles and affects how -Nchunk is calculated, which in turn affects the chunk IDs assigned -to each atom. It is useful for converting a "sparse" set of chunk IDs -(with many IDs that have no atoms assigned to them), into a "dense" -set of IDs, where every chunk has one or more atoms assigned to it. -

    -

    Two possible use cases are as follows. If a large simulation box is -mostly empty space, then the binning style may produce many bins -with no atoms. If compress is set to yes, only bins with atoms -will be contribute to Nchunk. Likewise, the molecule or -compute/fix/variable styles may produce large Nchunk values. For -example, the compute cluster/atom command -assigns every atom an atom ID for one of the atoms it is clustered -with. For a million-atom system with 5 clusters, there would only be -5 unique chunk IDs, but the largest chunk ID might be 1 million, -resulting in Nchunk = 1 million. If compress is set to yes, -Nchunk will be reset to 5. -

    -

    If compress is set to no, which is the default, no compression is -done. If it is set to yes, all chunk IDs with no atoms are removed -from the list of chunk IDs, and the list is sorted. The remaining -chunk IDs are renumbered from 1 to Nchunk where Nchunk is the new -length of the list. The chunk IDs assigned to each atom reflect -the new renumbering from 1 to Nchunk. -

    -

    The original chunk IDs (before renumbering) can be accessed by the -compute property/chunk command and its -id keyword, or by the fix ave/chunk command -which outputs the original IDs as one of the columns in its global -output array. For example, using the "compute cluster/atom" command -discussed above, the original 5 unique chunk IDs might be atom IDs -(27,4982,58374,857838,1000000). After compresion, these will be -renumbered to (1,2,3,4,5). The original values (27,...,1000000) can -be output to a file by the fix ave/chunk command, -or by using the fix ave/time command in -conjunction with the compute -property/chunk command. -

    -

    IMPORTANT NOTE: The compression operation requires global -communication across all processors to share their chunk ID values. -It can require large memory on every processor to store them, even -after they are compressed, if there are are a large number of unique -chunk IDs with atoms assigned to them. It uses a STL map to find -unique chunk IDs and store them in sorted order. Each time an atom is -assigned a compressed chunk ID, it must access the STL map. All of -this means that compression can be expensive, both in memory and CPU -time. The use of the limit keyword in conjunction with the -compress keyword can affect these costs, depending on which keyword -is used first. So use this option with care. -

    -
    - -

    The discard keyword applies to all chunk styles. It affects what -chunk IDs are assigned to atoms that do not match one of the valid -chunk IDs from 1 to Nchunk. Note that it does not apply to atoms -that are not in the specified group or optionally specified region. -Those atoms are always assigned a chunk ID = 0. -

    -

    If the calculated chunk ID for an atom is not within the range 1 to -Nchunk then it is a "discard" atom. Note that Nchunk may have -been shrunk by the limit keyword. Or the compress keyword may -have eliminated chunk IDs that were valid before the compression took -place, and are now not in the compressed list. Also note that for the -molecule chunk style, if new molecules are added to the system, -their chunk IDs may exceed a previously calculated Nchunk. -Likewise, evaluation of a compute/fix/variable on a later timestep may -return chunk IDs that are invalid for the previously calculated -Nchunk. -

    -

    All the chunk styles except the binning styles, must use discard -set to either yes or no. If discard is set to yes, which is -the default, then every "discard" atom has its chunk ID set to 0. If -discard is set to no, every "discard" atom has its chunk ID set to -Nchunk. I.e. it becomes part of the last chunk. -

    -

    The binning styles use the discard keyword to decide whether to -discard atoms outside the spatial domain covered by bins, or to assign -them to the bin they are nearest to. Details are as follows. -

    -

    If discard is set to yes, an out-of-domain atom will have its -chunk ID set to 0. If discard is set to no, the atom will have -its chunk ID set to the first or last bin in that dimension. If -(discard is set to mixed, which is the default, it will only have -its chunk ID set to the first or last bin if bins extend to the -simulation box boundary in that dimension. This is the case if the -bound keyword settings are lower and upper, which is the -default. If the bound keyword settings are numeric values, then the -atom will have its chunk ID set to 0 if it is outside the bounds of -any bin. Note that in this case, it is possible that the first or -last bin extends beyond the numeric bounds settings, depending on -the specified origin. If this is the case, the chunk ID of the atom -is only set to 0 if it is outside the first or last bin, not if it is -simply outside the numeric bounds setting. -

    -
    - -

    The bound keyword only applies to the binning styles; otherwise it -is ignored. It can be used one or more times to limit the extent of -bin coverage in a specified dimension, i.e. to only bin a portion of -the box. If the lo setting is lower or the hi setting is -upper, the bin extent in that direction extends to the box boundary. -If a numeric value is used for lo and/or hi, then the bin extent -in the lo or hi direction extends only to that value, which is -assumed to be inside (or at least near) the simulation box boundaries, -though LAMMPS does not check for this. Note that using the bound -keyword typically reduces the total number of bins and thus the number -of chunks Nchunk. -

    -

    The units keyword only applies to the binning styles; otherwise it -is ignored. It determines the meaning of the distance units used for -the bin sizes delta and for origin and bounds values if they are -coordinate values. For orthogonal simulation boxes, any of the 3 -options may be used. For non-orthogonal (triclinic) simulation boxes, -only the reduced option may be used. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacing. A reduced value means normalized -unitless values between 0 and 1, which represent the lower and upper -faces of the simulation box respectively. Thus an origin value of -0.5 means the center of the box in any dimension. A delta value of -0.1 means 10 bins span the box in that dimension. -

    -
    - -
    - -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values are unitless chunk IDs, ranging from 1 to -Nchunk (inclusive) for atoms assigned to chunks, and 0 for atoms not -belonging to a chunk. -

    -

    Restrictions: -

    -

    Even if the nchunk keyword is set to once, the chunk IDs assigned -to each atom are not stored in a restart files. This means you cannot -expect those assignments to persist in a restarted simulation. -Instead you must re-specify this command and assign atoms to chunks when -the restarted simulation begins. -

    -

    Related commands: -

    -

    fix ave/chunk -

    -

    Default: -

    -

    The option defaults are as follows: -

    -
    • region = none -
    • nchunk = every if compress is yes, overriding other defaults listed here -
    • nchunk = once for type style -
    • nchunk = once for mol style if region is none -
    • nchunk = every for mol style if region is set -
    • nchunk = once for binning style if the simulation box size is static or units = reduced -
    • nchunk = every for binning style if the simulation box size is dynamic and units is lattice or box -
    • nchunk = every for compute/fix/variable style -
    • limit = 0 -
    • ids = every -
    • compress = no -
    • discard = yes for all styles except binning -
    • discard = mixed for binning styles -
    • bound = lower and upper in all dimensions -
    • units = lattice -
    - diff --git a/doc/doc2/compute_cluster_atom.html b/doc/doc2/compute_cluster_atom.html deleted file mode 100644 index 9bf8ce34ad..0000000000 --- a/doc/doc2/compute_cluster_atom.html +++ /dev/null @@ -1,78 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute cluster/atom command -

    -

    Syntax: -

    -
    compute ID group-ID cluster/atom cutoff 
-
    -
    • ID, group-ID are documented in compute command -
    • cluster/atom = style name of this compute command -
    • cutoff = distance within which to label atoms as part of same cluster (distance units) -
    -

    Examples: -

    -
    compute 1 all cluster/atom 1.0 
-
    -

    Description: -

    -

    Define a computation that assigns each atom a cluster ID. -

    -

    A cluster is defined as a set of atoms, each of which is within the -cutoff distance from one or more other atoms in the cluster. If an -atom has no neighbors within the cutoff distance, then it is a 1-atom -cluster. The ID of every atom in the cluster will be the smallest -atom ID of any atom in the cluster. -

    -

    Only atoms in the compute group are clustered and assigned cluster -IDs. Atoms not in the compute group are assigned a cluster ID = 0. -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each of a -clsuter/atom style. -

    -

    IMPORTANT NOTE: If you have a bonded system, then the settings of -special_bonds command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the special_bonds -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included when computing the clusters. This -does not apply when using long-range coulomb (coul/long, coul/msm, -coul/wolf or similar. One way to get around this would be to set -special_bond scaling factors to very tiny numbers that are not exactly -zero (e.g. 1.0e-50). Another workaround is to write a dump file, and -use the rerun command to compute the clusters for -snapshots in the dump file. The rerun script can use a -special_bonds command that includes all pairs in -the neighbor list. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be an ID > 0, as explained above. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute coord/atom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_cna_atom.html b/doc/doc2/compute_cna_atom.html deleted file mode 100644 index 191b8911c8..0000000000 --- a/doc/doc2/compute_cna_atom.html +++ /dev/null @@ -1,104 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute cna/atom command -

    -

    Syntax: -

    -
    compute ID group-ID cna/atom cutoff 
-
    -
    • ID, group-ID are documented in compute command -
    • cna/atom = style name of this compute command -
    • cutoff = cutoff distance for nearest neighbors (distance units) -
    -

    Examples: -

    -
    compute 1 all cna/atom 3.08 
-
    -

    Description: -

    -

    Define a computation that calculates the CNA (Common Neighbor -Analysis) pattern for each atom in the group. In solid-state systems -the CNA pattern is a useful measure of the local crystal structure -around an atom. The CNA methodology is described in (Faken) -and (Tsuzuki). -

    -

    Currently, there are five kinds of CNA patterns LAMMPS recognizes: -

    -
    • fcc = 1 -
    • hcp = 2 -
    • bcc = 3 -
    • icosohedral = 4 -
    • unknown = 5 -
    -

    The value of the CNA pattern will be 0 for atoms not in the specified -compute group. Note that normally a CNA calculation should only be -performed on mono-component systems. -

    -

    The CNA calculation can be sensitive to the specified cutoff value. -You should insure the appropriate nearest neighbors of an atom are -found within the cutoff distance for the presumed crystal strucure. -E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest -neighbors for perfect BCC crystals. These formulas can be used to -obtain a good cutoff distance: -

    -
    -
    -

    where a is the lattice constant for the crystal structure concerned -and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a -for HCP crystals. -

    -

    Also note that since the CNA calculation in LAMMPS uses the neighbors -of an owned atom to find the nearest neighbors of a ghost atom, the -following relation should also be satisfied: -

    -
    -
    -

    where Rc is the cutoff distance of the potential, Rs is the skin -distance as specified by the neighbor command, and -cutoff is the argument used with the compute cna/atom command. LAMMPS -will issue a warning if this is not the case. -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (e.g. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each with a -cna/atom style. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be a number from 0 to 5, as explained -above. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute centro/atom -

    -

    Default: none -

    -
    - - - -

    (Faken) Faken, Jonsson, Comput Mater Sci, 2, 279 (1994). -

    - - -

    (Tsuzuki) Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). -

    - diff --git a/doc/doc2/compute_com.html b/doc/doc2/compute_com.html deleted file mode 100644 index 64735c5cf5..0000000000 --- a/doc/doc2/compute_com.html +++ /dev/null @@ -1,62 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute com command -

    -

    Syntax: -

    -
    compute ID group-ID com 
-
    -
    • ID, group-ID are documented in compute command -
    • com = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all com 
-
    -

    Description: -

    -

    Define a computation that calculates the center-of-mass of the group -of atoms, including all effects due to atoms passing thru periodic -boundaries. -

    -

    A vector of three quantites is calculated by this compute, which -are the x,y,z coordinates of the center of mass. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to the -center-of-mass in "unwrapped" form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    Output info: -

    -

    This compute calculates a global vector of length 3, which can be -accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector values are "intensive". The vector values will be in -distance units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute com/chunk -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_com_chunk.html b/doc/doc2/compute_com_chunk.html deleted file mode 100644 index a2ad970b71..0000000000 --- a/doc/doc2/compute_com_chunk.html +++ /dev/null @@ -1,92 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute com/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID com/chunk chunkID 
-
    -
    • ID, group-ID are documented in compute command -
    • com/chunk = style name of this compute command -
    • chunkID = ID of compute chunk/atom command -
    -

    Examples: -

    -
    compute 1 fluid com/chunk molchunk 
-
    -

    Description: -

    -

    Define a computation that calculates the center-of-mass for multiple -chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates the x,y,z coordinates of the center-of-mass -for each chunk, which includes all effects due to atoms passing thru -periodic boundaries. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's -center-of-mass in "unwrapped" form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    The simplest way to output the results of the compute com/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array where the number of rows = the -number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The number of columns = -3 for the x,y,z center-of-mass coordinates of each chunk. These -values can be accessed by any command that uses global array values -from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The array values are "intensive". The array values will be in -distance units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute com -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_contact_atom.html b/doc/doc2/compute_contact_atom.html deleted file mode 100644 index 6c35adf5b0..0000000000 --- a/doc/doc2/compute_contact_atom.html +++ /dev/null @@ -1,59 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute contact/atom command -

    -

    Syntax: -

    -
    compute ID group-ID contact/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • contact/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all contact/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the number of contacts -for each atom in a group. -

    -

    The contact number is defined for finite-size spherical particles as -the number of neighbor atoms which overlap the central particle, -meaning that their distance of separation is less than or equal to the -sum of the radii of the two particles. -

    -

    The value of the contact number will be 0.0 for atoms not in the -specified compute group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, whose values can be -accessed by any command that uses per-atom values from a compute as -input. See Section_howto 15 for an -overview of LAMMPS output options. -

    -

    The per-atom vector values will be a number >= 0.0, as explained -above. -

    -

    Restrictions: -

    -

    This compute requires that atoms store a radius as defined by the -atom_style sphere command. -

    -

    Related commands: -

    -

    compute coord/atom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_coord_atom.html b/doc/doc2/compute_coord_atom.html deleted file mode 100644 index 98dbe794f9..0000000000 --- a/doc/doc2/compute_coord_atom.html +++ /dev/null @@ -1,97 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute coord/atom command -

    -

    Syntax: -

    -
    compute ID group-ID coord/atom cutoff type1 type2 ... 
-
    -
    • ID, group-ID are documented in compute command -
    • coord/atom = style name of this compute command -
    • cutoff = distance within which to count coordination neighbors (distance units) -
    • typeN = atom type for Nth coordination count (see asterisk form below) -
    -

    Examples: -

    -
    compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 * 
-
    -

    Description: -

    -

    Define a computation that calculates one or more coordination numbers -for each atom in a group. -

    -

    A coordination number is defined as the number of neighbor atoms with -specified atom type(s) that are within the specified cutoff distance -from the central atom. Atoms not in the group are included in a -coordination number of atoms in the group. -

    -

    The typeN keywords allow you to specify which atom types contribute -to each coordination number. One coordination number is computed for -each of the typeN keywords listed. If no typeN keywords are -listed, a single coordination number is calculated, which includes -atoms of all types (same as the "*" format, see below). -

    -

    The typeN keywords can be specified in one of two ways. An explicit -numeric value can be used, as in the 2nd example above. Or a -wild-card asterisk can be used to specify a range of atom types. This -takes the form "*" or "*n" or "n*" or "m*n". If N = the number of -atom types, then an asterisk with no numeric values means all types -from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). -

    -

    The value of all coordination numbers will be 0.0 for atoms not in the -specified compute group. -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. -

    -

    IMPORTANT NOTE: If you have a bonded system, then the settings of -special_bonds command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the special_bonds -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the coordination count. One way -to get around this, is to write a dump file, and use the -rerun command to compute the coordination for snapshots -in the dump file. The rerun script can use a -special_bonds command that includes all pairs in -the neighbor list. -

    -

    Output info: -

    -

    If single type1 keyword is specified (or if none are specified), -this compute calculates a per-atom vector. If multiple typeN -keywords are specified, this compute calculates a per-atom array, with -N columns. These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The per-atom vector or array values will be a number >= 0.0, as -explained above. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute cluster/atom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_damage_atom.html b/doc/doc2/compute_damage_atom.html deleted file mode 100644 index d475631308..0000000000 --- a/doc/doc2/compute_damage_atom.html +++ /dev/null @@ -1,68 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute damage/atom command -

    -

    Syntax: -

    -
    compute ID group-ID damage/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • damage/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all damage/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom damage for each atom -in a group. This is a quantity relevant for Peridynamics -models. See this document -for an overview of LAMMPS commands for Peridynamics modeling. -

    -

    The "damage" of a Peridymaics particles is based on the bond breakage -between the particle and its neighbors. If all the bonds are broken -the particle is considered to be fully damaged. -

    -

    See the PDLAMMPS user -guide for a formal -definition of "damage" and more details about Peridynamics as it is -implemented in LAMMPS. -

    -

    This command can be used with all the Peridynamic pair styles. -

    -

    The damage value will be 0.0 for atoms not in the specified compute -group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values are unitlesss numbers (damage) >= 0.0. -

    -

    Restrictions: -

    -

    This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute dilatation, compute -plasticity -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_dihedral_local.html b/doc/doc2/compute_dihedral_local.html deleted file mode 100644 index b8d4bb5674..0000000000 --- a/doc/doc2/compute_dihedral_local.html +++ /dev/null @@ -1,79 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute dihedral/local command -

    -

    Syntax: -

    -
    compute ID group-ID dihedral/local input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • dihedral/local = style name of this compute command - -
    • one or more keywords may be appended - -
    • keyword = phi - -
        phi = tabulate dihedral angles 
-
      - -
    -

    Examples: -

    -
    compute 1 all dihedral/local phi 
-
    -

    Description: -

    -

    Define a computation that calculates properties of individual dihedral -interactions. The number of datums generated, aggregated across all -processors, equals the number of angles in the system, modified by the -group parameter as explained below. -

    -

    The local data stored by this command is generated by looping over all -the atoms owned on a processor and their dihedrals. A dihedral will -only be included if all 4 atoms in the dihedral are in the specified -compute group. -

    -

    Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, dihedral output from the compute -property/local command can be combined -with data from this command and output by the dump local -command in a consistent way. -

    -

    Output info: -

    -

    This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of dihedrals. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The output for phi will be in degrees. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump local, compute -property/local -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_dilatation_atom.html b/doc/doc2/compute_dilatation_atom.html deleted file mode 100644 index 2f76dee3ba..0000000000 --- a/doc/doc2/compute_dilatation_atom.html +++ /dev/null @@ -1,71 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute dilatation/atom command -

    -

    Syntax: -

    -
    compute ID group-ID dilatation/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • dilation/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all dilatation/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom dilatation for each -atom in a group. This is a quantity relevant for Peridynamics -models. See this document -for an overview of LAMMPS commands for Peridynamics modeling. -

    -

    For small deformation, dilatation of is the measure of the volumetric -strain. -

    -

    The dilatation "theta" for each peridynamic particle I is calculated -as a sum over its neighbors with unbroken bonds, where the -contribution of the IJ pair is a function of the change in bond length -(versus the initial length in the reference state), the volume -fraction of the particles and an influence function. See the -PDLAMMPS user -guide for a formal -definition of dilatation. -

    -

    This command can only be used with a subset of the Peridynamic pair -styles: peri/lps, peri/ves and peri/eps. -

    -

    The dilatation value will be 0.0 for atoms not in the specified -compute group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of LAMMPS output options. -

    -

    The per-atom vector values are unitlesss numbers (theta) >= 0.0. -

    -

    Restrictions: -

    -

    This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute damage, compute -plasticity -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_displace_atom.html b/doc/doc2/compute_displace_atom.html deleted file mode 100644 index 87370be662..0000000000 --- a/doc/doc2/compute_displace_atom.html +++ /dev/null @@ -1,74 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute displace/atom command -

    -

    Syntax: -

    -
    compute ID group-ID displace/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • displace/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all displace/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the current displacement of each -atom in the group from its original coordinates, including all effects -due to atoms passing thru periodic boundaries. -

    -

    A vector of four quantites per atom is calculated by this compute. -The first 3 elements of the vector are the dx,dy,dz displacements. -The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + -dz*dz). -

    -

    The displacement of an atom is from its original position at the time -the compute command was issued. The value of the displacement will be -0.0 for atoms not in the specified compute group. -

    -

    IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by -using the image flags associated with each atom. See the dump -custom command for a discussion of "unwrapped" coordinates. -See the Atoms section of the read_data command for a -discussion of image flags and how they are set for each atom. You can -reset the image flags (e.g. to 0) before invoking this compute by -using the set image command. -

    -

    IMPORTANT NOTE: If you want the quantities calculated by this compute -to be continuous when running from a restart file, -then you should use the same ID for this compute, as in the original -run. This is so that the fix this compute creates to store per-atom -quantities will also have the same ID, and thus be initialized -correctly with time=0 atom coordinates from the restart file. -

    -

    Output info: -

    -

    This compute calculates a per-atom array with 4 columns, which can be -accessed by indices 1-4 by any command that uses per-atom values from -a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The per-atom array values will be in distance units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute msd, dump custom, fix -store/state -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_erotate_asphere.html b/doc/doc2/compute_erotate_asphere.html deleted file mode 100644 index 8ea9a4e1dc..0000000000 --- a/doc/doc2/compute_erotate_asphere.html +++ /dev/null @@ -1,75 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute erotate/asphere command -

    -

    Syntax: -

    -
    compute ID group-ID erotate/asphere 
-
    -
    • ID, group-ID are documented in compute command -
    • erotate/asphere = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all erotate/asphere 
-
    -

    Description: -

    -

    Define a computation that calculates the rotational kinetic energy of -a group of aspherical particles. The aspherical particles can be -ellipsoids, or line segments, or triangles. See the -atom_style and read_data commands -for descriptions of these options. -

    -

    For all 3 types of particles, the rotational kinetic energy is -computed as 1/2 I w^2, where I is the inertia tensor for the -aspherical particle and w is its angular velocity, which is computed -from its angular momentum if needed. -

    -

    IMPORTANT NOTE: For 2d models, ellipsoidal particles -are treated as ellipsoids, not ellipses, meaning their moments of -inertia will be the same as in 3d. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the KE). This value can be -used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an -overview of LAMMPS output options. -

    -

    The scalar value calculated by this compute is "extensive". The -scalar value will be in energy units. -

    -

    Restrictions: -

    -

    This compute requires that ellipsoidal particles atoms store a shape -and quaternion orientation and angular momentum as defined by the -atom_style ellipsoid command. -

    -

    This compute requires that line segment particles atoms store a length -and orientation and angular velocity as defined by the atom_style -line command. -

    -

    This compute requires that triangular particles atoms store a size and -shape and quaternion orientation and angular momentum as defined by -the atom_style tri command. -

    -

    All particles in the group must be finite-size. They cannot be point -particles. -

    -

    Related commands: none -

    -

    compute erotate/sphere -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_erotate_rigid.html b/doc/doc2/compute_erotate_rigid.html deleted file mode 100644 index 2e4358e30a..0000000000 --- a/doc/doc2/compute_erotate_rigid.html +++ /dev/null @@ -1,66 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute erotate/rigid command -

    -

    Syntax: -

    -
    compute ID group-ID erotate/rigid fix-ID 
-
    -
    • ID, group-ID are documented in compute command -
    • erotate/rigid = style name of this compute command -
    • fix-ID = ID of rigid body fix -
    -

    Examples: -

    -
    compute 1 all erotate/rigid myRigid 
-
    -

    Description: -

    -

    Define a computation that calculates the rotational kinetic energy of -a collection of rigid bodies, as defined by one of the fix -rigid command variants. -

    -

    The rotational energy of each rigid body is computed as 1/2 I Wbody^2, -where I is the inertia tensor for the rigid body, and Wbody is its -angular velocity vector. Both I and Wbody are in the frame of -reference of the rigid body, i.e. I is diagonalized. -

    -

    The fix-ID should be the ID of one of the fix rigid -commands which defines the rigid bodies. The group specified in the -compute command is ignored. The rotational energy of all the rigid -bodies defined by the fix rigid command in included in the -calculation. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the summed rotational energy -of all the rigid bodies). This value can be used by any command that -uses a global scalar value from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The scalar value calculated by this compute is "extensive". The -scalar value will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute ke/rigid -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_erotate_sphere.html b/doc/doc2/compute_erotate_sphere.html deleted file mode 100644 index eb6662b13b..0000000000 --- a/doc/doc2/compute_erotate_sphere.html +++ /dev/null @@ -1,62 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute erotate/sphere command -

    -

    Syntax: -

    -
    compute ID group-ID erotate/sphere 
-
    -
    • ID, group-ID are documented in compute command -
    • erotate/sphere = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all erotate/sphere 
-
    -

    Description: -

    -

    Define a computation that calculates the rotational kinetic energy of -a group of spherical particles. -

    -

    The rotational energy is computed as 1/2 I w^2, where I is the moment -of inertia for a sphere and w is the particle's angular velocity. -

    -

    IMPORTANT NOTE: For 2d models, particles are treated -as spheres, not disks, meaning their moment of inertia will be the -same as in 3d. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the KE). This value can be -used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an -overview of LAMMPS output options. -

    -

    The scalar value calculated by this compute is "extensive". The -scalar value will be in energy units. -

    -

    Restrictions: -

    -

    This compute requires that atoms store a radius and angular velocity -(omega) as defined by the atom_style sphere command. -

    -

    All particles in the group must be finite-size spheres or point -particles. They cannot be aspherical. Point particles will not -contribute to the rotational energy. -

    -

    Related commands: -

    -

    compute erotate/asphere -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_erotate_sphere_atom.html b/doc/doc2/compute_erotate_sphere_atom.html deleted file mode 100644 index e758b7be4f..0000000000 --- a/doc/doc2/compute_erotate_sphere_atom.html +++ /dev/null @@ -1,58 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute erotate/sphere/atom command -

    -

    Syntax: -

    -
    compute ID group-ID erotate/sphere/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • erotate/sphere/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all erotate/sphere/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the rotational kinetic energy for -each particle in a group. -

    -

    The rotational energy is computed as 1/2 I w^2, where I is the moment -of inertia for a sphere and w is the particle's angular velocity. -

    -

    IMPORTANT NOTE: For 2d models, particles are treated -as spheres, not disks, meaning their moment of inertia will be the -same as in 3d. -

    -

    The value of the rotational kinetic energy will be 0.0 for atoms not -in the specified compute group or for point particles with a radius = -0.0. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump custom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_event_displace.html b/doc/doc2/compute_event_displace.html deleted file mode 100644 index 8efff145ad..0000000000 --- a/doc/doc2/compute_event_displace.html +++ /dev/null @@ -1,67 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute event/displace command -

    -

    Syntax: -

    -
    compute ID group-ID event/displace threshold 
-
    -
    • ID, group-ID are documented in compute command -
    • event/displace = style name of this compute command -
    • threshold = minimum distance anyparticle must move to trigger an event (distance units) -
    -

    Examples: -

    -
    compute 1 all event/displace 0.5 
-
    -

    Description: -

    -

    Define a computation that flags an "event" if any particle in the -group has moved a distance greater than the specified threshold -distance when compared to a previously stored reference state -(i.e. the previous event). This compute is typically used in -conjunction with the prd and tad commands, -to detect if a transition -to a new minimum energy basin has occurred. -

    -

    This value calculated by the compute is equal to 0 if no particle has -moved far enough, and equal to 1 if one or more particles have moved -further than the threshold distance. -

    -

    NOTE: If the system is undergoing significant center-of-mass motion, -due to thermal motion, an external force, or an initial net momentum, -then this compute will not be able to distinguish that motion from -local atom displacements and may generate "false postives." -

    -

    Output info: -

    -

    This compute calculates a global scalar (the flag). This value can be -used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an -overview of LAMMPS output options. -

    -

    The scalar value calculated by this compute is "intensive". The -scalar value will be a 0 or 1 as explained above. -

    -

    Restrictions: -

    -

    This command can only be used if LAMMPS was built with the REPLICA -package. See the Making LAMMPS section -for more info on packages. -

    -

    Related commands: -

    -

    prd, tad -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_fep.html b/doc/doc2/compute_fep.html deleted file mode 100644 index 6eecc4b023..0000000000 --- a/doc/doc2/compute_fep.html +++ /dev/null @@ -1,279 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute fep command -

    -

    Syntax: -

    -
    compute ID group-ID fep temp attribute args ... keyword value ... 
-
    -
    • ID, group-ID are documented in the compute command - -
    • fep = name of this compute command - -
    • temp = external temperature (as specified for constant-temperature run) - -
    • one or more attributes with args may be appended - -
    • attribute = pair or atom - -
        pair args = pstyle pparam I J v_delta
-    pstyle = pair style name, e.g. lj/cut
-    pparam = parameter to perturb
-    I,J = type pair(s) to set parameter for
-    v_delta = variable with perturbation to apply (in the units of the parameter)
-  atom args = aparam I v_delta
-    aparam = parameter to perturb
-    I = type to set parameter for
-    v_delta = variable with perturbation to apply (in the units of the parameter) 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = tail or volume - -
        tail value = no or yes
-    no = ignore tail correction to pair energies (usually small in fep)
-    yes = include tail correction to pair energies
-  volume value = no or yes
-    no = ignore volume changes (e.g. in NVE or NVT trajectories)
-    yes = include volume changes (e.g. in NpT trajectories) 
-
      - -
    -

    Examples: -

    -
    compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
-compute 1 all fep 300 atom charge 2 v_delta 
-
    -

    Description: -

    -

    Apply a perturbation to parameters of the interaction potential and -recalculate the pair potential energy without changing the atomic -coordinates from those of the reference, unperturbed system. This -compute can be used to calculate free energy differences using several -methods, such as free-energy perturbation (FEP), finite-difference -thermodynamic integration (FDTI) or Bennet's acceptance ratio method -(BAR). -

    -

    The potential energy of the system is decomposed in three terms: a -background term corresponding to interaction sites whose parameters -remain constant, a reference term U0 corresponding to the -initial interactions of the atoms that will undergo perturbation, and -a term U1 corresponding to the final interactions of -these atoms: -

    -
    -
    -

    A coupling parameter λ varying from 0 to 1 connects the -reference and perturbed systems: -

    -
    -
    -

    It is possible but not necessary that the coupling parameter (or a -function thereof) appears as a multiplication factor of the potential -energy. Therefore, this compute can apply perturbations to interaction -parameters that are not directly proportional to the potential energy -(e.g. σ in Lennard-Jones potentials). -

    -

    This command can be combined with fix adapt to -perform multistage free-energy perturbation calculations along -stepwise alchemical transformations during a simulation run: -

    -
    -
    -

    This compute is suitable for the finite-difference thermodynamic -integration (FDTI) method (Mezei), which is based on an -evaluation of the numerical derivative of the free energy by a -perturbation method using a very small δ: -

    -
    -
    -

    where wi are weights of a numerical quadrature. The fix -adapt command can be used to define the stages of -λ at which the derivative is calculated and averaged. -

    -

    The compute fep calculates the exponential Boltzmann term and also the -potential energy difference U1-U0. By -choosing a very small perturbation δ the thermodynamic -integration method can be implemented using a numerical evaluation of -the derivative of the potential energy with respect to λ: -

    -
    -
    -

    Another technique to calculate free energy differences is the -acceptance ratio method (Bennet), which can be implemented -by calculating the potential energy differences with δ = 1.0 on -both the forward and reverse routes: -

    -
    -
    -

    The value of the free energy difference is determined by numerical -root finding to establish the equality. -

    -

    Concerning the choice of how the atomic parameters are perturbed in -order to setup an alchemical transformation route, several strategies -are available, such as single-topology or double-topology strategies -(Pearlman). The latter does not require modification of -bond lengths, angles or other internal coordinates. -

    -

    IMPORTANT NOTES: This compute command does not take kinetic energy -into account, therefore the masses of the particles should not be -modified between the reference and perturbed states, or along the -alchemical transformation route. This compute command does not change -bond lengths or other internal coordinates (Boresch, -Karplus). -

    -
    - -

    The pair attribute enables various parameters of potentials defined -by the pair_style and pair_coeff -commands to be changed, if the pair style supports it. -

    -

    The pstyle argument is the name of the pair style. For example, -pstyle could be specified as "lj/cut". The pparam argument is the -name of the parameter to change. This is a (non-exclusive) list of -pair styles and parameters that can be used with this compute. See -the doc pages for individual pair styles and their energy formulas for -the meaning of these parameters: -

    -
    - - - - - - - - - - - - -
    lj/cut epsilon,sigma type pairs
    lj/cut/coul/cut epsilon,sigma type pairs
    lj/cut/coul/long epsilon,sigma type pairs
    lj/cut/soft epsilon,sigma,lambda type pairs
    coul/cut/soft lambda type pairs
    coul/long/soft lambda type pairs
    lj/cut/coul/cut/soft epsilon,sigma,lambda type pairs
    lj/cut/coul/long/soft epsilon,sigma,lambda type pairs
    lj/cut/tip4p/long/soft epsilon,sigma,lambda type pairs
    tip4p/long/soft lambda type pairs
    lj/charmm/coul/long/soft epsilon,sigma,lambda type pairs
    born a,b,c type pairs
    buck a,c type pairs -
    - -

    Note that it is easy to add new potentials and their parameters to -this list. All it typically takes is adding an extract() method to -the pair_*.cpp file associated with the potential. -

    -

    Similar to the pair_coeff command, I and J can be -specified in one of two ways. Explicit numeric values can be used for -each, as in the 1st example above. I <= J is required. LAMMPS sets -the coefficients for the symmetric J,I interaction to the same -values. A wild-card asterisk can be used in place of or in conjunction -with the I,J arguments to set the coefficients for multiple pairs of -atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = -the number of atom types, then an asterisk with no numeric values -means all types from 1 to N. A leading asterisk means all types from -1 to n (inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. -

    -

    If pair_style hybrid or hybrid/overlay is being -used, then the pstyle will be a sub-style name. You must specify -I,J arguments that correspond to type pair values defined (via the -pair_coeff command) for that sub-style. -

    -

    The v_name argument for keyword pair is the name of an -equal-style variable which will be evaluated each time -this compute is invoked. It should be specified as v_name, where name -is the variable name. -

    -
    - -

    The atom attribute enables atom properties to be changed. The -aparam argument is the name of the parameter to change. This is the -current list of atom parameters that can be used with this compute: -

    -
    • charge = charge on particle -
    -

    The v_name argument for keyword pair is the name of an -equal-style variable which will be evaluated each time -this compute is invoked. It should be specified as v_name, where name -is the variable name. -

    -
    - -

    The tail keyword controls the calculation of the tail correction to -"van der Waals" pair energies beyond the cutoff, if this has been -activated via the pair_modify command. If the -perturbation is small, the tail contribution to the energy difference -between the reference and perturbed systems should be negligible. -

    -

    If the keyword volume = yes, then the Boltzmann term is multiplied -by the volume so that correct ensemble averaging can be performed over -trajectories during which the volume fluctuates or changes (Allen and -Tildesley): -

    -
    -
    -
    - -

    Output info: -

    -

    This compute calculates a global vector of length 3 which contains the -energy difference (U1-U0) as c_ID[1], the -Boltzmann factor exp(-(U1-U0)/kT), or -Vexp(-(U1-U0)/kT), as c_ID[2] and the -volume of the simulation box V as c_ID[3]. U1 is the -pair potential energy obtained with the perturbed parameters and -U0 is the pair potential energy obtained with the -unperturbed parameters. The energies include kspace terms if these -are used in the simulation. -

    -

    These output results can be used by any command that uses a global -scalar or vector from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. For example, the computed values can be averaged using fix -ave/time. -

    -

    The values calculated by this compute are "extensive". -

    -

    Restrictions: -

    -

    This compute is distributed as the USER-FEP package. It is only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix adapt/fep, fix ave/time, -pair_lj_soft_coul_soft -

    -

    Default: -

    -

    The option defaults are tail = no, volume = no. -

    -
    - - - -

    (Pearlman) Pearlman, J Chem Phys, 98, 1487 (1994) -

    - - -

    (Mezei) Mezei, J Chem Phys, 86, 7084 (1987) -

    - - -

    (Bennet) Bennet, J Comput Phys, 22, 245 (1976) -

    - - -

    (BoreschKarplus) Boresch and Karplus, J Phys Chem A, 103, 103 (1999) -

    - - -

    (AllenTildesley) Allen and Tildesley, Computer Simulation of -Liquids, Oxford University Press (1987) -

    - diff --git a/doc/doc2/compute_group_group.html b/doc/doc2/compute_group_group.html deleted file mode 100644 index 268b1f68ca..0000000000 --- a/doc/doc2/compute_group_group.html +++ /dev/null @@ -1,135 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute group/group command -

    -

    Syntax: -

    -
    compute ID group-ID group/group group2-ID keyword value ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • group/group = style name of this compute command - -
    • group2-ID = group ID of second (or same) group - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = pair or kspace or boundary - -
        pair value = yes or no
-  kspace value = yes or no
-  boundary value = yes or no 
-
      - -
    -

    Examples: -

    -
    compute 1 lower group/group upper
-compute 1 lower group/group upper kspace yes
-compute mine fluid group/group wall 
-
    -

    Description: -

    -

    Define a computation that calculates the total energy and force -interaction between two groups of atoms: the compute group and the -specified group2. The two groups can be the same. -

    -

    If the pair keyword is set to yes, which is the default, then the -the interaction energy will include a pair component which is defined -as the pairwise energy between all pairs of atoms where one atom in -the pair is in the first group and the other is in the second group. -Likewise, the interaction force calculated by this compute will -include the force on the compute group atoms due to pairwise -interactions with atoms in the specified group2. -

    -

    If the kspace keyword is set to yes, which is not the default, and -if a kspace_style is defined, then the interaction -energy will include a Kspace component which is the long-range -Coulombic energy between all the atoms in the first group and all the -atoms in the 2nd group. Likewise, the interaction force calculated by -this compute will include the force on the compute group atoms due to -long-range Coulombic interactions with atoms in the specified group2. -

    -

    Normally the long-range Coulombic energy converges only when the net -charge of the unit cell is zero. However, one can assume the net -charge of the system is neutralized by a uniform background plasma, -and a correction to the system energy can be applied to reduce -artifacts. For more information see (Bogusz). If the -boundary keyword is set to yes, which is the default, and kspace -contributions are included, then this energy correction term will be -added to the total group-group energy. This correction term does not -affect the force calculation and will be zero if one or both of the -groups are charge neutral. This energy correction term is the same as -that included in the regular Ewald and PPPM routines. -

    -

    This compute does not calculate any bond or angle or dihedral or -improper interactions between atoms in the two groups. -

    -
    - -

    The pairwise contributions to the group-group interactions are -calculated by looping over a neighbor list. The Kspace contribution -to the group-group interactions require essentially the same amount of -work (FFTs, Ewald summation) as computing long-range forces for the -entire system. Thus it can be costly to invoke this compute too -frequently. -

    -

    If you desire a breakdown of the interactions into a pairwise and -Kspace component, simply invoke the compute twice with the appropriate -yes/no settings for the pair and kspace keywords. This is no more -costly than using a single compute with both keywords set to yes. -The individual contributions can be summed in a -variable if desired. -

    -

    This document describes how the long-range -group-group calculations are performed. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the energy) and a global -vector of length 3 (force), which can be accessed by indices 1-3. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    Both the scalar and vector values calculated by this compute are -"extensive". The scalar value will be in energy units. -The vector values will be in force units. -

    -

    Restrictions: -

    -

    Not all pair styles can be evaluated in a pairwise mode as required by -this compute. For example, 3-body and other many-body potentials, -such as Tersoff and -Stillinger-Weber cannot be used. EAM -potentials only include the pair potential portion of the EAM -interaction when used by this compute, not the embedding term. -

    -

    Not all Kspace styles support calculation of group/group interactions. -The ewald and pppm styles do. -

    -

    Related commands: none -

    -

    Default: -

    -

    The option defaults are pair = yes, kspace = no, and boundary = yes. -

    -
    - - - -

    Bogusz et al, J Chem Phys, 108, 7070 (1998) -

    - diff --git a/doc/doc2/compute_gyration.html b/doc/doc2/compute_gyration.html deleted file mode 100644 index 8d0eed96f2..0000000000 --- a/doc/doc2/compute_gyration.html +++ /dev/null @@ -1,78 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute gyration command -

    -

    Syntax: -

    -
    compute ID group-ID gyration 
-
    -
    • ID, group-ID are documented in compute command -
    • gyration = style name of this compute command -
    -

    Examples: -

    -
    compute 1 molecule gyration 
-
    -

    Description: -

    -

    Define a computation that calculates the radius of gyration Rg of the -group of atoms, including all effects due to atoms passing thru -periodic boundaries. -

    -

    Rg is a measure of the size of the group of atoms, and is computed as -the square root of the Rg^2 value in this formula -

    -
    -
    -

    where M is the total mass of the group, Rcm is the center-of-mass -position of the group, and the sum is over all atoms in the group. -

    -

    A Rg^2 tensor, stored as a 6-element vector, is also calculated by -this compute. The formula for the components of the tensor is the -same as the above formula, except that (Ri - Rcm)^2 is replaced by -(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 -components of the vector are ordered xx, yy, zz, xy, xz, yz. Note -that unlike the scalar Rg, each of the 6 values of the tensor is -effectively a "squared" value, since the cross-terms may be negative -and taking a sqrt() would be invalid. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to Rg in -"unwrapped" form, by using the image flags associated with each atom. -See the dump custom command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    Output info: -

    -

    This compute calculates a global scalar (Rg) and a global vector of -length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These -values can be used by any command that uses a global scalar value or -vector values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The scalar and vector values calculated by this compute are -"intensive". The scalar and vector values will be in distance and -distance^2 units respectively. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute gyration/chunk -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_gyration_chunk.html b/doc/doc2/compute_gyration_chunk.html deleted file mode 100644 index 61f391f8ff..0000000000 --- a/doc/doc2/compute_gyration_chunk.html +++ /dev/null @@ -1,122 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute gyration/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID gyration/chunk chunkID keyword value ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • gyration/chunk = style name of this compute command - -
    • chunkID = ID of compute chunk/atom command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = tensor - -
        tensor value = none 
-
      - -
    -

    Examples: -

    -
    compute 1 molecule gyration/chunk molchunk
-compute 2 molecule gyration/chunk molchunk tensor 
-
    -

    Description: -

    -

    Define a computation that calculates the radius of gyration Rg for -multiple chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates the radius of gyration Rg for each chunk, -which includes all effects due to atoms passing thru periodic -boundaries. -

    -

    Rg is a measure of the size of a chunk, and is computed by this -formula -

    -
    -
    -

    where M is the total mass of the chunk, Rcm is the center-of-mass -position of the chunk, and the sum is over all atoms in the -chunk. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    If the tensor keyword is specified, then the scalar Rg value is not -calculated, but an Rg tensor is instead calculated for each chunk. -The formula for the components of the tensor is the same as the above -formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy - -Rcmy) for the xy component, etc. The 6 components of the tensor are -ordered xx, yy, zz, xy, xz, yz. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to Rg in -"unwrapped" form, by using the image flags associated with each atom. -See the dump custom command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    The simplest way to output the results of the compute gyration/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all gyration/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global vector if the tensor keyword is not -specified and a global array if it is. The length of the vector or -number of rows in the array = the number of chunks Nchunk as -calculated by the specified compute -chunk/atom command. If the tensor keyword -is specified, the global array has 6 columns. The vector or array can -be accessed by any command that uses global values from a compute as -input. See this section for an overview -of LAMMPS output options. -

    -

    All the vector or array values calculated by this compute are -"intensive". The vector or array values will be in distance -units, since they are the square root of values -represented by the formula above. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    compute gyration -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_heat_flux.html b/doc/doc2/compute_heat_flux.html deleted file mode 100644 index 8ea72a590e..0000000000 --- a/doc/doc2/compute_heat_flux.html +++ /dev/null @@ -1,192 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute heat/flux command -

    -

    Syntax: -

    -
    compute ID group-ID heat/flux ke-ID pe-ID stress-ID 
-
    -
    • ID, group-ID are documented in compute command -
    • heat/flux = style name of this compute command -
    • ke-ID = ID of a compute that calculates per-atom kinetic energy -
    • pe-ID = ID of a compute that calculates per-atom potential energy -
    • stress-ID = ID of a compute that calculates per-atom stress -
    -

    Examples: -

    -
    compute myFlux all heat/flux myKE myPE myStress 
-
    -

    Description: -

    -

    Define a computation that calculates the heat flux vector based on -contributions from atoms in the specified group. This can be used by -itself to measure the heat flux into or out of a reservoir of atoms, -or to calculate a thermal conductivity using the Green-Kubo formalism. -

    -

    See the fix thermal/conductivity -command for details on how to compute thermal conductivity in an -alternate way, via the Muller-Plathe method. See the fix -heat command for a way to control the heat added or -subtracted to a group of atoms. -

    -

    The compute takes three arguments which are IDs of other -computes. One calculates per-atom kinetic energy -(ke-ID), one calculates per-atom potential energy (pe-ID), and the -third calcualtes per-atom stress (stress-ID). These should be -defined for the same group used by compute heat/flux, though LAMMPS -does not check for this. -

    -

    The Green-Kubo formulas relate the ensemble average of the -auto-correlation of the heat flux J to the thermal conductivity kappa: -

    -
    -
    -
    -
    -

    Ei in the first term of the equation for J is the per-atom energy -(potential and kinetic). This is calculated by the computes ke-ID -and pe-ID. Si in the second term of the equation for J is the -per-atom stress tensor calculated by the compute stress-ID. The -tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a -vector. Note that as discussed below, the 1/V scaling factor in the -equation for J is NOT included in the calculation performed by this -compute; you need to add it for a volume appropriate to the atoms -included in the calculation. -

    -

    IMPORTANT NOTE: The compute pe/atom and -compute stress/atom commands have options -for which terms to include in their calculation (pair, bond, etc). -The heat flux calculation will thus include exactly the same terms. -Normally you should use compute stress/atom -virial so as not to include a kinetic energy -term in the heat flux. -

    -

    This compute calculates 6 quantities and stores them in a 6-component -vector. The first 3 components are the x, y, z components of the full -heat flux vector, i.e. (Jx, Jy, Jz). The next 3 components are the x, -y, z components of just the convective portion of the flux, i.e. the -first term in the equation for J above. -

    -
    - -

    The heat flux can be output every so many timesteps (e.g. via the -thermo_style custom command). Then as a -post-processing operation, an autocorrelation can be performed, its -integral estimated, and the Green-Kubo formula above evaluated. -

    -

    The fix ave/correlate command can calclate -the autocorrelation. The trap() function in the -variable command can calculate the integral. -

    -

    An example LAMMPS input script for solid Ar is appended below. The -result should be: average conductivity ~0.29 in W/mK. -

    -
    - -

    Output info: -

    -

    This compute calculates a global vector of length 6 (total heat flux -vector, followed by convective heat flux vector), which can be -accessed by indices 1-6. These values can be used by any command that -uses global vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector values calculated by this compute are "extensive", meaning -they scale with the number of atoms in the simulation. They can be -divided by the appropriate volume to get a flux, which would then be -an "intensive" value, meaning independent of the number of atoms in -the simulation. Note that if the compute is "all", then the -appropriate volume to divide by is the simulation box volume. -However, if a sub-group is used, it should be the volume containing -those atoms. -

    -

    The vector values will be in energy*velocity units. Once -divided by a volume the units will be that of flux, namely -energy/area/time units -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix thermal/conductivity, -fix ave/correlate, -variable -

    -

    Default: none -

    -
    - -
    # Sample LAMMPS input script for thermal conductivity of solid Ar 
-
    -
    units       real
-variable    T equal 70
-variable    V equal vol
-variable    dt equal 4.0
-variable    p equal 200     # correlation length
-variable    s equal 10      # sample interval
-variable    d equal $p*$s   # dump interval 
-
    -
    # convert from LAMMPS real units to SI 
-
    -
    variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
-variable    kCal2J equal 4186.0/6.02214e23
-variable    A2m equal 1.0e-10
-variable    fs2s equal 1.0e-15
-variable    convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m} 
-
    -
    # setup problem 
-
    -
    dimension    3
-boundary     p p p
-lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
-region       box block 0 4 0 4 0 4
-create_box   1 box
-create_atoms 1 box
-mass	     1 39.948
-pair_style   lj/cut 13.0
-pair_coeff   * * 0.2381 3.405
-timestep     ${dt}
-thermo	     $d 
-
    -
    # equilibration and thermalization 
-
    -
    velocity     all create $T 102486 mom yes rot yes dist gaussian
-fix          NVT all nvt temp $T $T 10 drag 0.2
-run          8000 
-
    -
    # thermal conductivity calculation, switch to NVE if desired 
-
    -
    #unfix       NVT
-#fix         NVE all nve 
-
    -
    reset_timestep 0
-compute      myKE all ke/atom
-compute      myPE all pe/atom
-compute      myStress all stress/atom NULL virial
-compute      flux all heat/flux myKE myPE myStress
-variable     Jx equal c_flux[1]/vol
-variable     Jy equal c_flux[2]/vol
-variable     Jz equal c_flux[3]/vol
-fix          JJ all ave/correlate $s $p $d &
-             c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running
-variable     scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt}
-variable     k11 equal trap(f_JJ[3])*${scale}
-variable     k22 equal trap(f_JJ[4])*${scale}
-variable     k33 equal trap(f_JJ[5])*${scale}
-thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
-run          100000
-variable     k equal (v_k11+v_k22+v_k33)/3.0
-variable     ndens equal count(all)/vol
-print        "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3" 
-
    - diff --git a/doc/doc2/compute_hexorder_atom.html b/doc/doc2/compute_hexorder_atom.html deleted file mode 100644 index 344d1c7a7f..0000000000 --- a/doc/doc2/compute_hexorder_atom.html +++ /dev/null @@ -1,125 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute hexorder/atom command -

    -

    Syntax: -

    -
    compute ID group-ID hexorder/atom keyword values ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • hexorder/atom = style name of this compute command - -
    • one or more keyword/value pairs may be appended - -
      keyword = degree or nnn or cutoff 
-  cutoff value = distance cutoff
-  nnn value = number of nearest neighbors
-  degree value = degree n of order parameter 
-
      - -
    -

    Examples: -

    -
    compute 1 all hexorder/atom 
-compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 
-
    -

    Description: -

    -

    Define a computation that calculates qn the bond-orientational -order parameter for each atom in a group. The hexatic (n = 6) order -parameter was introduced by Nelson and Halperin as a way to detect -hexagonal symmetry in two-dimensional systems. For each atom, qn -is a complex number (stored as two real numbers) defined as follows: -

    -
    -
    -

    where the sum is over the nnn nearest neighbors -of the central atom. The angle theta -is formed by the bond vector rij and the x axis. theta is calculated -only using the x and y components, whereas the distance from the -central atom is calculated using all three -x, y, and z components of the bond vector. -Neighbor atoms not in the group -are included in the order parameter of atoms in the group. -

    -

    The optional keyword cutoff defines the distance cutoff -used when searching for neighbors. The default value, also -the maximum allowable value, is the cutoff specified -by the pair style. -

    -

    The optional keyword nnn defines the number of nearest -neighbors used to calculate qn. The default value is 6. -If the value is NULL, then all neighbors up to the -distance cutoff are used. -

    -

    The optional keyword degree sets the degree n of the order parameter. -The default value is 6. For a perfect hexagonal lattice with -nnn = 6, -q6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 -depends only on the orientation of the lattice relative to the x axis. -In an isotropic liquid, local neighborhoods may still exhibit -weak hexagonal symmetry, but because the orientational correlation -decays quickly with distance, the value of phi will be different for -different atoms, and so when q6 is averaged over all the atoms -in the system, |<q6>| << 1. -

    -

    The value of qn is set to zero for atoms not in the -specified compute group, as well as for atoms that have less than -nnn neighbors within the distance cutoff. -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. -

    -

    IMPORTANT NOTE: If you have a bonded system, then the settings of -special_bonds command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the special_bonds -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the order parameter. This difficulty -can be circumvented by writing a dump file, and using the -rerun command to compute the order parameter for snapshots -in the dump file. The rerun script can use a -special_bonds command that includes all pairs in -the neighbor list. -

    -

    Output info: -

    -

    This compute calculates a per-atom array with 2 columns, giving the -real and imaginary parts qn, a complex number restricted to the -unit disk of the complex plane i.e. Re(qn)^2 + Im(qn)^2 <= 1 . -

    -

    These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute orientorder/atom, compute coord/atom, compute centro/atom -

    -

    Default: -

    -

    The option defaults are cutoff = pair style cutoff, nnn = 6, degree = 6 -

    -
    - - - -

    (Nelson) Nelson, Halperin, Phys Rev B, 19, 2457 (1979). -

    - diff --git a/doc/doc2/compute_improper_local.html b/doc/doc2/compute_improper_local.html deleted file mode 100644 index cdf58f1b6e..0000000000 --- a/doc/doc2/compute_improper_local.html +++ /dev/null @@ -1,79 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute improper/local command -

    -

    Syntax: -

    -
    compute ID group-ID improper/local input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • improper/local = style name of this compute command - -
    • one or more keywords may be appended - -
    • keyword = chi - -
        chi = tabulate improper angles 
-
      - -
    -

    Examples: -

    -
    compute 1 all improper/local chi 
-
    -

    Description: -

    -

    Define a computation that calculates properties of individual improper -interactions. The number of datums generated, aggregated across all -processors, equals the number of impropers in the system, modified by -the group parameter as explained below. -

    -

    The local data stored by this command is generated by looping over all -the atoms owned on a processor and their impropers. An improper will -only be included if all 4 atoms in the improper are in the specified -compute group. -

    -

    Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, improper output from the compute -property/local command can be combined -with data from this command and output by the dump local -command in a consistent way. -

    -

    Output info: -

    -

    This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of impropers. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The output for chi will be in degrees. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump local, compute -property/local -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_inertia_chunk.html b/doc/doc2/compute_inertia_chunk.html deleted file mode 100644 index 9b131c32a0..0000000000 --- a/doc/doc2/compute_inertia_chunk.html +++ /dev/null @@ -1,93 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute inertia/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID inertia/chunk chunkID 
-
    -
    • ID, group-ID are documented in compute command -
    • inertia/chunk = style name of this compute command -
    • chunkID = ID of compute chunk/atom command -
    -

    Examples: -

    -
    compute 1 fluid inertia/chunk molchunk 
-
    -

    Description: -

    -

    Define a computation that calculates the inertia tensor for multiple -chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates the 6 components of the symmetric intertia -tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The -calculation includes all effects due to atoms passing thru periodic -boundaries. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's -inertia tensor in "unwrapped" form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    The simplest way to output the results of the compute inertia/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all inertia/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array where the number of rows = the -number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The number of columns = -6 for the 6 components of the inertia tensor for each chunk, ordered -as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The array values are "intensive". The array values will be in -mass*distance^2 units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    variable inertia() function -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_ke.html b/doc/doc2/compute_ke.html deleted file mode 100644 index 90497bec8d..0000000000 --- a/doc/doc2/compute_ke.html +++ /dev/null @@ -1,64 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute ke command -

    -

    Syntax: -

    -
    compute ID group-ID ke 
-
    -
    • ID, group-ID are documented in compute command -
    • ke = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all ke 
-
    -

    Description: -

    -

    Define a computation that calculates the translational kinetic energy -of a group of particles. -

    -

    The kinetic energy of each particle is computed as 1/2 m v^2, where m -and v are the mass and velocity of the particle. -

    -

    There is a subtle difference between the quantity calculated by this -compute and the kinetic energy calculated by the ke or etotal -keyword used in thermodynamic output, as specified by the -thermo_style command. For this compute, kinetic -energy is "translational" kinetic energy, calculated by the simple -formula above. For thermodynamic output, the ke keyword infers -kinetic energy from the temperature of the system with 1/2 Kb T of -energy for each degree of freedom. For the default temperature -computation via the compute temp command, these -are the same. But different computes that calculate temperature can -subtract out different non-thermal components of velocity and/or -include different degrees of freedom (translational, rotational, etc). -

    -

    Output info: -

    -

    This compute calculates a global scalar (the summed KE). This value -can be used by any command that uses a global scalar value from a -compute as input. See Section_howto 15 -for an overview of LAMMPS output options. -

    -

    The scalar value calculated by this compute is "extensive". The -scalar value will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute erotate/sphere -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_ke_atom.html b/doc/doc2/compute_ke_atom.html deleted file mode 100644 index fdf97f197a..0000000000 --- a/doc/doc2/compute_ke_atom.html +++ /dev/null @@ -1,53 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute ke/atom command -

    -

    Syntax: -

    -
    compute ID group-ID ke/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • ke/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all ke/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom translational -kinetic energy for each atom in a group. -

    -

    The kinetic energy is simply 1/2 m v^2, where m is the mass and v is -the velocity of each atom. -

    -

    The value of the kinetic energy will be 0.0 for atoms not in the -specified compute group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump custom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_ke_atom_eff.html b/doc/doc2/compute_ke_atom_eff.html deleted file mode 100644 index d305890bba..0000000000 --- a/doc/doc2/compute_ke_atom_eff.html +++ /dev/null @@ -1,82 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute ke/atom/eff command -

    -

    Syntax: -

    -
    compute ID group-ID ke/atom/eff 
-
    -
    • ID, group-ID are documented in compute command -
    • ke/atom/eff = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all ke/atom/eff 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom translational -(nuclei and electrons) and radial kinetic energy (electron only) in a -group. The particles are assumed to be nuclei and electrons modeled -with the electronic force field. -

    -

    The kinetic energy for each nucleus is computed as 1/2 m v^2, where m -corresponds to the corresponding nuclear mass, and the kinetic energy -for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me -and v correspond to the mass and translational velocity of each -electron, and s to its radial velocity, respectively. -

    -

    There is a subtle difference between the quantity calculated by this -compute and the kinetic energy calculated by the ke or etotal -keyword used in thermodynamic output, as specified by the -thermo_style command. For this compute, kinetic -energy is "translational" plus electronic "radial" kinetic energy, -calculated by the simple formula above. For thermodynamic output, the -ke keyword infers kinetic energy from the temperature of the system -with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in -eFF. -

    -

    IMPORTANT NOTE: The temperature in eFF should be monitored via the -compute temp/eff command, which can be printed -with thermodynamic output by using the -thermo_modify command, as shown in the following -example: -

    -
    compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press 
-thermo_modify   temp effTemp 
-
    -

    The value of the kinetic energy will be 0.0 for atoms (nuclei or -electrons) not in the specified compute group. -

    -

    Output info: -

    -

    This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom computes as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    dump custom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_ke_eff.html b/doc/doc2/compute_ke_eff.html deleted file mode 100644 index 7c476b9aa6..0000000000 --- a/doc/doc2/compute_ke_eff.html +++ /dev/null @@ -1,83 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute ke/eff command -

    -

    Syntax: -

    -
    compute ID group-ID ke/eff 
-
    -
    • ID, group-ID are documented in compute command -
    • ke/eff = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all ke/eff 
-
    -

    Description: -

    -

    Define a computation that calculates the kinetic energy of motion of a -group of eFF particles (nuclei and electrons), as modeled with the -electronic force field. -

    -

    The kinetic energy for each nucleus is computed as 1/2 m v^2 and the -kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me -s^2), where m corresponds to the nuclear mass, me to the electron -mass, v to the translational velocity of each particle, and s to the -radial velocity of the electron, respectively. -

    -

    There is a subtle difference between the quantity calculated by this -compute and the kinetic energy calculated by the ke or etotal -keyword used in thermodynamic output, as specified by the -thermo_style command. For this compute, kinetic -energy is "translational" and "radial" (only for electrons) kinetic -energy, calculated by the simple formula above. For thermodynamic -output, the ke keyword infers kinetic energy from the temperature of -the system with 1/2 Kb T of energy for each degree of freedom. For -the eFF temperature computation via the compute -temp_eff command, these are the same. But -different computes that calculate temperature can subtract out -different non-thermal components of velocity and/or include other -degrees of freedom. -

    -

    IMPRORTANT NOTE: The temperature in eFF models should be monitored via -the compute temp/eff command, which can be -printed with thermodynamic output by using the -thermo_modify command, as shown in the following -example: -

    -
    compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press 
-thermo_modify   temp effTemp 
-
    -

    See compute temp/eff. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the KE). This value can be -used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an -overview of LAMMPS output options. -

    -

    The scalar value calculated by this compute is "extensive". The -scalar value will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_ke_rigid.html b/doc/doc2/compute_ke_rigid.html deleted file mode 100644 index 485cf37fa3..0000000000 --- a/doc/doc2/compute_ke_rigid.html +++ /dev/null @@ -1,65 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute ke/rigid command -

    -

    Syntax: -

    -
    compute ID group-ID ke/rigid fix-ID 
-
    -
    • ID, group-ID are documented in compute command -
    • ke = style name of this compute command -
    • fix-ID = ID of rigid body fix -
    -

    Examples: -

    -
    compute 1 all ke/rigid myRigid 
-
    -

    Description: -

    -

    Define a computation that calculates the translational kinetic energy -of a collection of rigid bodies, as defined by one of the fix -rigid command variants. -

    -

    The kinetic energy of each rigid body is computed as 1/2 M Vcm^2, -where M is the total mass of the rigid body, and Vcm is its -center-of-mass velocity. -

    -

    The fix-ID should be the ID of one of the fix rigid -commands which defines the rigid bodies. The group specified in the -compute command is ignored. The kinetic energy of all the rigid -bodies defined by the fix rigid command in included in the -calculation. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the summed KE of all the -rigid bodies). This value can be used by any command that uses a -global scalar value from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "extensive". The -scalar value will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute erotate/rigid -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_meso_e_atom.html b/doc/doc2/compute_meso_e_atom.html deleted file mode 100644 index 3350eb3000..0000000000 --- a/doc/doc2/compute_meso_e_atom.html +++ /dev/null @@ -1,61 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute meso_e/atom command -

    -

    Syntax: -

    -
    compute ID group-ID meso_e/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • meso_e/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all meso_e/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom internal energy -for each atom in a group. -

    -

    The internal energy is the energy associated with the internal degrees -of freedom of a mesoscopic particles, e.g. a Smooth-Particle -Hydrodynamics particle. -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The value of the internal energy will be 0.0 for atoms not in the -specified compute group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    dump custom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_meso_rho_atom.html b/doc/doc2/compute_meso_rho_atom.html deleted file mode 100644 index 790e2f9005..0000000000 --- a/doc/doc2/compute_meso_rho_atom.html +++ /dev/null @@ -1,61 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute meso_rho/atom command -

    -

    Syntax: -

    -
    compute ID group-ID meso_rho/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • meso_rho/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all meso_rho/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom mesoscopic density -for each atom in a group. -

    -

    The mesoscopic density is the mass density of a mesoscopic particle, -calculated by kernel function interpolation using "pair style -sph/rhosum". -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The value of the mesoscopic density will be 0.0 for atoms not in the -specified compute group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be in mass/volume units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    dump custom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_meso_t_atom.html b/doc/doc2/compute_meso_t_atom.html deleted file mode 100644 index 39b21ccff9..0000000000 --- a/doc/doc2/compute_meso_t_atom.html +++ /dev/null @@ -1,63 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute meso_t/atom command -

    -

    Syntax: -

    -
    compute ID group-ID meso_t/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • meso_t/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all meso_t/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom internal temperature -for each atom in a group. -

    -

    The internal temperature is the ratio of internal energy over the heat -capacity associated with the internal degrees of freedom of a mesoscopic -particles, e.g. a Smooth-Particle Hydrodynamics particle. -

    -

    T_int = E_int / C_V, int -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The value of the internal energy will be 0.0 for atoms not in the -specified compute group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be in temperature units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    dump custom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_modify.html b/doc/doc2/compute_modify.html deleted file mode 100644 index 4536ee76bc..0000000000 --- a/doc/doc2/compute_modify.html +++ /dev/null @@ -1,80 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute_modify command -

    -

    Syntax: -

    -
    compute_modify compute-ID keyword value ... 
-
    -
    • compute-ID = ID of the compute to modify - -
    • one or more keyword/value pairs may be listed - -
    • keyword = extra or dynamic - -
        extra value = N
-    N = # of extra degrees of freedom to subtract
-  dynamic value = yes or no
-    yes/no = do or do not recompute the number of atoms contributing to the temperature
-  thermo value = yes or no
-    yes/no = do or do not add contributions from fixes to the potential energy 
-
      - -
    -

    Examples: -

    -
    compute_modify myTemp extra 0
-compute_modify newtemp dynamic yes extra 600 
-
    -

    Description: -

    -

    Modify one or more parameters of a previously defined compute. Not -all compute styles support all parameters. -

    -

    The extra keyword refers to how many degrees-of-freedom are -subtracted (typically from 3N) as a normalizing factor in a -temperature computation. Only computes that compute a temperature use -this option. The default is 2 or 3 for 2d or 3d -systems which is a correction factor for an ensemble -of velocities with zero total linear momentum. You can use a negative -number for the extra parameter if you need to add -degrees-of-freedom. See the compute -temp/asphere command for an example. -

    -

    The dynamic keyword determines whether the number of atoms N in the -compute group is re-computed each time a temperature is computed. -Only compute styles that compute a temperature use this option. By -default, N is assumed to be constant. If you are adding atoms to the -system (see the fix pour or fix -deposit commands) or expect atoms to be lost -(e.g. due to evaporation), then this option should be used to insure -the temperature is correctly normalized. -

    -

    The thermo keyword determines whether the potential energy -contribution calculated by some fixes is added to the -potential energy calculated by the compute. Currently, only the -compute of style pe uses this option. See the doc pages for -individual fixes for details. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute -

    -

    Default: -

    -

    The option defaults are extra = 2 or 3 for 2d or 3d systems and -dynamic = no. Thermo is yes if the compute of style pe was -defined with no extra keywords; otherwise it is no. -

    - diff --git a/doc/doc2/compute_msd.html b/doc/doc2/compute_msd.html deleted file mode 100644 index 5c01e1a716..0000000000 --- a/doc/doc2/compute_msd.html +++ /dev/null @@ -1,127 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute msd command -

    -

    Syntax: -

    -
    compute ID group-ID msd keyword values ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • msd = style name of this compute command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = com or average - -
        com value = yes or no
-  average value = yes or no 
-
      - -
    -

    Examples: -

    -
    compute 1 all msd
-compute 1 upper msd com yes average yes 
-
    -

    Description: -

    -

    Define a computation that calculates the mean-squared displacement -(MSD) of the group of atoms, including all effects due to atoms -passing thru periodic boundaries. For computation of the non-Gaussian -parameter of mean-squared displacement, see the compute -msd/nongauss command. -

    -

    A vector of four quantites is calculated by this compute. The first 3 -elements of the vector are the squared dx,dy,dz displacements, summed -and averaged over atoms in the group. The 4th element is the total -squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and -averaged over atoms in the group. -

    -

    The slope of the mean-squared displacement (MSD) versus time is -proportional to the diffusion coefficient of the diffusing atoms. -

    -

    The displacement of an atom is from its reference position. This is -normally the original position at the time -the compute command was issued, unless the average keyword is set to yes. -The value of the displacement will be -0.0 for atoms not in the specified compute group. -

    -

    If the com option is set to yes then the effect of any drift in -the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calculated. -

    -

    If the average option is set to yes then the reference position of -an atom is based on the average position of that atom, -corrected for center-of-mass motion if requested. -The average position -is a running average over all previous calls to the compute, including the -current call. So on the first call -it is current position, on the second call it is the arithmetic average of the -current position and the position on the first call, and so on. -Note that when using this option, the precise value of the mean square -displacement will depend on the number of times the compute is -called. So, for example, changing the frequency of thermo output may -change the computed displacement. Also, the precise values will be -changed if a single simulation is broken up into two parts, using -either multiple run commands or a restart file. It only makes -sense to use this option if the atoms are not diffusing, so that -their average positions relative to the center of mass of the system -are stationary. The most common case is crystalline solids undergoing -thermal motion. -

    -

    IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by -using the image flags associated with each atom. See the dump -custom command for a discussion of "unwrapped" coordinates. -See the Atoms section of the read_data command for a -discussion of image flags and how they are set for each atom. You can -reset the image flags (e.g. to 0) before invoking this compute by -using the set image command. -

    -

    IMPORTANT NOTE: If you want the quantities calculated by this compute -to be continuous when running from a restart file, -then you should use the same ID for this compute, as in the original -run. This is so that the fix this compute creates to store per-atom -quantities will also have the same ID, and thus be initialized -correctly with atom reference positions from the restart file. -When average is set to yes, then the atom reference positions -are restored correctly, but not the number of samples used -obtain them. As a result, the reference positions from the restart -file are combined with subsequent positions as if they were from a -single sample, instead of many, which will change the values of msd -somewhat. -

    -

    Output info: -

    -

    This compute calculates a global vector of length 4, which can be -accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector values are "intensive". The vector values will be in -distance^2 units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute msd/nongauss, compute -displace_atom, fix -store/state, compute -msd/chunk -

    -

    Default: -

    -

    The option default are com = no, average = no. -

    - diff --git a/doc/doc2/compute_msd_chunk.html b/doc/doc2/compute_msd_chunk.html deleted file mode 100644 index e6ef5bc252..0000000000 --- a/doc/doc2/compute_msd_chunk.html +++ /dev/null @@ -1,125 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute msd/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID msd/chunk chunkID 
-
    -
    • ID, group-ID are documented in compute command -
    • msd/chunk = style name of this compute command -
    • chunkID = ID of compute chunk/atom command -
    -

    Examples: -

    -
    compute 1 all msd/chunk molchunk 
-
    -

    Description: -

    -

    Define a computation that calculates the mean-squared displacement -(MSD) for multiple chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    Four quantites are calculated by this compute for each chunk. The -first 3 quantities are the squared dx,dy,dz displacements of the -center-of-mass. The 4th component is the total squared displacement, -i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These -calculations include all effects due to atoms passing thru periodic -boundaries. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    The slope of the mean-squared displacement (MSD) versus time is -proportional to the diffusion coefficient of the diffusing chunks. -

    -

    The displacement of the center-of-mass of the chunk is from its -original center-of-mass position, calculated on the timestep this -compute command was first invoked. -

    -

    IMPORTANT NOTE: The number of chunks Nchunk calculated by the -compute chunk/atom command must remain -constant each time this compute is invoked, so that the displacement -for each chunk from its original position can be computed -consistently. If Nchunk does not remain constant, an error will be -generated. If needed, you can enforce a constant Nchunk by using -the nchunk once or ids once options when specifying the compute -chunk/atom command. -

    -

    IMPORTANT NOTE: This compute stores the original position (of the -center-of-mass) of each chunk. When a displacement is calculated on a -later timestep, it is assumed that the same atoms are assigned to the -same chunk ID. However LAMMPS has no simple way to insure this is the -case, though you can use the ids once option when specifying the -compute chunk/atom command. Note that if -this is not the case, the MSD calculation does not have a sensible -meaning. -

    -

    IMPORTANT NOTE: The initial coordinates of the atoms in each chunk are -stored in "unwrapped" form, by using the image flags associated with -each atom. See the dump custom command for a discussion -of "unwrapped" coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    IMPORTANT NOTE: Unlike the compute msd command, -this compute does not store the initial center-of-mass coorindates of -its molecules in a restart file. Thus you cannot continue the MSD per -chunk calculation of this compute when running from a restart -file. -

    -

    The simplest way to output the results of the compute com/msd -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all com/msd cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array where the number of rows = the -number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The number of columns = -4 for dx,dy,dz and the total displacement. These values can be -accessed by any command that uses global array values from a compute -as input. See this section for an -overview of LAMMPS output options. -

    -

    The array values are "intensive". The array values will be in -distance^2 units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute msd -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_msd_nongauss.html b/doc/doc2/compute_msd_nongauss.html deleted file mode 100644 index e041a30796..0000000000 --- a/doc/doc2/compute_msd_nongauss.html +++ /dev/null @@ -1,90 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute msd/nongauss command -

    -

    Syntax: -

    -
    compute ID group-ID msd/nongauss keyword values ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • msd/nongauss = style name of this compute command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = com - -
        com value = yes or no 
-
      - -
    -

    Examples: -

    -
    compute 1 all msd/nongauss
-compute 1 upper msd/nongauss com yes 
-
    -

    Description: -

    -

    Define a computation that calculates the mean-squared displacement -(MSD) and non-Gaussian parameter (NGP) of the group of atoms, -including all effects due to atoms passing thru periodic boundaries. -

    -

    A vector of three quantites is calculated by this compute. The first -element of the vector is the total squared dx,dy,dz displacements -drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the -fourth power of these displacements drfourth = (dx*dx + dy*dy + -dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the -group. The 3rd component is the nonGaussian diffusion paramter NGP = -3*drfourth/(5*drsquared*drsquared), i.e. -

    -
    -
    -

    The NGP is a commonly used quantity in studies of dynamical -heterogeneity. Its minimum theoretical value (-0.4) occurs when all -atoms have the same displacement magnitude. NGP=0 for Brownian -diffusion, while NGP > 0 when some mobile atoms move faster than -others. -

    -

    If the com option is set to yes then the effect of any drift in -the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calcluated. -

    -

    See the compute msd doc page for further IMPORTANT -NOTES, which also apply to this compute. -

    -

    Output info: -

    -

    This compute calculates a global vector of length 3, which can be -accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector values are "intensive". The first vector value will be in -distance^2 units, the second is in distance^4 units, and -the 3rd is dimensionless. -

    -

    Restrictions: -

    -

    This compute is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute msd -

    -

    Default: -

    -

    The option default is com = no. -

    - diff --git a/doc/doc2/compute_omega_chunk.html b/doc/doc2/compute_omega_chunk.html deleted file mode 100644 index 3c553afbc8..0000000000 --- a/doc/doc2/compute_omega_chunk.html +++ /dev/null @@ -1,94 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute omega/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID omega/chunk chunkID 
-
    -
    • ID, group-ID are documented in compute command -
    • omega/chunk = style name of this compute command -
    • chunkID = ID of compute chunk/atom command -
    -

    Examples: -

    -
    compute 1 fluid omega/chunk molchunk 
-
    -

    Description: -

    -

    Define a computation that calculates the angular velocity (omega) of -multiple chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates the 3 components of the angular velocity -vector for each chunk, via the formula L = Iw where L is the angular -momentum vector of the chunk, I is its moment of inertia tensor, and w -is omega = angular velocity of the chunk. The calculation includes -all effects due to atoms passing thru periodic boundaries. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's -angular velocity in "unwrapped" form, by using the image flags -associated with each atom. See the dump custom command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the read_data command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    The simplest way to output the results of the compute omega/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all omega/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array where the number of rows = the -number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The number of columns = -3 for the 3 xyz components of the angular velocity for each chunk. -These values can be accessed by any command that uses global array -values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The array values are "intensive". The array values will be in -velocity/distance units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    variable omega() function -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_orientorder_atom.html b/doc/doc2/compute_orientorder_atom.html deleted file mode 100644 index 70b64f978e..0000000000 --- a/doc/doc2/compute_orientorder_atom.html +++ /dev/null @@ -1,131 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute orientorder/atom command -

    -

    Syntax: -

    -
    compute ID group-ID orientorder/atom keyword values ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • orientorder/atom = style name of this compute command - -
    • one or more keyword/value pairs may be appended - -
      keyword = cutoff or nnn or ql 
-  cutoff value = distance cutoff
-  nnn value = number of nearest neighbors
-  degrees values = nlvalues, l1, l2,...  
-
      - -
    -

    Examples: -

    -
    compute 1 all orientorder/atom 
-compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 
-
    -

    Description: -

    -

    Define a computation that calculates a set of bond-orientational -order parameters Ql for each atom in a group. These order parameters -were introduced by Steinhardt et al. as a way to -characterize the local orientational order in atomic structures. -For each atom, Ql is a real number defined as follows: -

    -
    -
    -

    The first equation defines the spherical harmonic order parameters. -These are complex number components of the 3D analog of the 2D order -parameter qn, which is implemented as LAMMPS compute -hexorder/atom. -The summation is over the nnn nearest -neighbors of the central atom. -The angles theta and phi are the standard spherical polar angles -defining the direction of the bond vector rij. -The second equation defines Ql, which is a -rotationally invariant scalar quantity obtained by summing -over all the components of degree l. -

    -

    The optional keyword cutoff defines the distance cutoff -used when searching for neighbors. The default value, also -the maximum allowable value, is the cutoff specified -by the pair style. -

    -

    The optional keyword nnn defines the number of nearest -neighbors used to calculate Ql. The default value is 12. -If the value is NULL, then all neighbors up to the -specified distance cutoff are used. -

    -

    The optional keyword degrees defines the list of order parameters to -be computed. The first argument nlvalues is the number of order -parameters. This is followed by that number of integers giving the -degree of each order parameter. Because Q2 and all odd-degree -order parameters are zero for atoms in cubic crystals -(see Steinhardt), the default order parameters -are Q4, Q6, Q8, Q10, and Q12. For the -FCC crystal with nnn=12, Q4 = sqrt(7/3)/8 = 0.19094.... -The numerical values of all order parameters up to Q12 -for a range of commonly encountered high-symmetry structures are given -in Table I of Mickel et al.. -

    -

    The value of Ql is set to zero for atoms not in the -specified compute group, as well as for atoms that have less than -nnn neighbors within the distance cutoff. -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. -

    -

    IMPORTANT NOTE: If you have a bonded system, then the settings of -special_bonds command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the special_bonds -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the order parameter. This difficulty -can be circumvented by writing a dump file, and using the -rerun command to compute the order parameter for snapshots -in the dump file. The rerun script can use a -special_bonds command that includes all pairs in -the neighbor list. -

    -

    Output info: -

    -

    This compute calculates a per-atom array with nlvalues columns, giving the -Ql values for each atom, which are real numbers on the range 0 <= Ql <= 1. -

    -

    These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute coord/atom, compute centro/atom, compute hexorder/atom -

    -

    Default: -

    -

    The option defaults are cutoff = pair style cutoff, nnn = 12, degrees = 5 4 6 8 9 10 12 i.e. Q4, Q6, Q8, Q10, and Q12. -

    -
    - - - -(Steinhardt) P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). - - -

    (Mickel) W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013). -

    - diff --git a/doc/doc2/compute_pair.html b/doc/doc2/compute_pair.html deleted file mode 100644 index b456d96ba6..0000000000 --- a/doc/doc2/compute_pair.html +++ /dev/null @@ -1,86 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute pair command -

    -

    Syntax: -

    -
    compute ID group-ID pair pstyle evalue 
-
    -
    • ID, group-ID are documented in compute command -
    • pair = style name of this compute command -
    • pstyle = style name of a pair style that calculates additional values -
    • evalue = epair or evdwl or ecoul or blank (optional setting) -
    -

    Examples: -

    -
    compute 1 all pair gauss
-compute 1 all pair lj/cut/coul/cut ecoul
-compute 1 all pair reax 
-
    -

    Description: -

    -

    Define a computation that extracts additional values calculated by a -pair style, sums them across processors, and makes them accessible for -output or further processing by other commands. The group specified -for this command is ignored. -

    -

    The specified pstyle must be a pair style used in your simulation -either by itself or as a sub-style in a pair_style hybrid or -hybrid/overlay command. -

    -

    The evalue setting is optional; it may be left off the command. All -pair styles tally a potential energy epair which may be broken into -two parts: evdwl and ecoul such that epair = evdwl + ecoul. -If the pair style calculates Coulombic interactions, their energy will -be tallied in ecoul. Everything else (whether it is a Lennard-Jones -style van der Waals interaction or not) is tallied in evdwl. If -evalue is specified as epair or left out, then epair is stored -as a global scalar by this compute. This is useful when using -pair_style hybrid if you want to know the portion -of the total energy contributed by one sub-style. If evalue is -specfied as evdwl or ecoul, then just that portion of the energy -is stored as a global scalar. -

    -

    Some pair styles tally additional quantities, e.g. a breakdown of -potential energy into a dozen or so components is tallied by the -pair_style reax commmand. These values (1 or more) -are stored as a global vector by this compute. See the doc page for -individual pair styles for info on these values. -

    -

    Output info: -

    -

    This compute calculates a global scalar which is epair or evdwl or -ecoul. If the pair style supports it, it also calculates a global -vector of length >= 1, as determined by the pair style. These values -can be used by any command that uses global scalar or vector values -from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar and vector values calculated by this compute are -"extensive". -

    -

    The scalar value will be in energy units. The vector -values will typically also be in energy units, but -see the doc page for the pair style for details. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute pe -

    -

    Default: -

    -

    The default for evalue is epair. -

    - diff --git a/doc/doc2/compute_pair_local.html b/doc/doc2/compute_pair_local.html deleted file mode 100644 index d7a17323bd..0000000000 --- a/doc/doc2/compute_pair_local.html +++ /dev/null @@ -1,127 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute pair/local command -

    -

    Syntax: -

    -
    compute ID group-ID pair/local input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • pair/local = style name of this compute command - -
    • zero or more keywords may be appended - -
    • keyword = dist or eng or force or fx or fy or fz or pN - -
        dist = pairwise distance
-  eng = pairwise energy
-  force = pairwise force
-  fx,fy,fz = components of pairwise force
-  pN = pair style specific quantities for allowed N values 
-
      - -
    -

    Examples: -

    -
    compute 1 all pair/local eng
-compute 1 all pair/local dist eng force
-compute 1 all pair/local dist eng fx fy fz
-compute 1 all pair/local dist fx fy fz p1 p2 p3 
-
    -

    Description: -

    -

    Define a computation that calculates properties of individual pairwise -interactions. The number of datums generated, aggregated across all -processors, equals the number of pairwise interactions in the system. -

    -

    The local data stored by this command is generated by looping over the -pairwise neighbor list. Info about an individual pairwise interaction -will only be included if both atoms in the pair are in the specified -compute group, and if the current pairwise distance is less than the -force cutoff distance for that interaction, as defined by the -pair_style and pair_coeff -commands. -

    -

    The output dist is the distance bewteen the pair of atoms. -

    -

    The output eng is the interaction energy for the pair of atoms. -

    -

    The output force is the force acting between the pair of atoms, -which is positive for a repulsive force and negative for an attractive -force. The outputs fx, fy, and fz are the xyz components of -force on atom I. -

    -

    A pair style may define additional pairwise quantities which can be -accessed as p1 to pN, where N is defined by the pair style. Most -pair styles do not define any additional quantities, so N = 0. An -example of ones that do are the granular pair styles -which calculate the tangential force between two particles and return -its components and magnitude acting on atom I for N = 1,2,3,4. See -individual pair styles for detils. -

    -

    The output dist will be in distance units. The output -eng will be in energy units. The outputs force, -fx, fy, and fz will be in force units. The output -pN will be in whatever units the pair style defines. -

    -

    Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, pair output from the compute -property/local command can be combined -with data from this command and output by the dump local -command in a consistent way. -

    -

    IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, -1-4 interactions within the molecular topology, their pairwise -interaction may be turned off, and thus they may not appear in the -neighbor list, and will not be part of the local data created by this -command. More specifically, this will be true of I,J pairs with a -weighting factor of 0.0; pairs with a non-zero weighting factor are -included. The weighting factors for 1-2, 1-3, and 1-4 pairwise -interactions are set by the special_bonds -command. An exception is if long-range Coulombics are being computed -via the kspace_style command, then atom pairs with -weighting factors of zero are still included in the neighbor list, so -that a portion of the long-range interaction contribution can be -computed in the pair style. Hence in that case, those atom pairs will -be part of the local data created by this command. -

    -

    Output info: -

    -

    This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of pairs. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The output for dist will be in distance units. The -output for eng will be in energy units. The output for -force will be in force units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump local, compute -property/local -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_pe.html b/doc/doc2/compute_pe.html deleted file mode 100644 index 86171a28e0..0000000000 --- a/doc/doc2/compute_pe.html +++ /dev/null @@ -1,109 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute pe command -

    -

    compute pe/cuda command -

    -

    Syntax: -

    -
    compute ID group-ID pe keyword ... 
-
    -
    • ID, group-ID are documented in compute command -
    • pe = style name of this compute command -
    • zero or more keywords may be appended -
    • keyword = pair or bond or angle or dihedral or improper or kspace -
    -

    Examples: -

    -
    compute 1 all pe
-compute molPE all pe bond angle dihedral improper 
-
    -

    Description: -

    -

    Define a computation that calculates the potential energy of the -entire system of atoms. The specified group must be "all". See the -compute pe/atom command if you want per-atom -energies. These per-atom values could be summed for a group of atoms -via the compute reduce command. -

    -

    The energy is calculated by the various pair, bond, etc potentials -defined for the simulation. If no extra keywords are listed, then the -potential energy is the sum of pair, bond, angle, dihedral, improper, -and kspace (long-range) energy. If any extra keywords are listed, -then only those components are summed to compute the potential energy. -

    -

    The Kspace contribution requires 1 extra FFT each timestep the energy -is calculated, if using the PPPM solver via the kspace_style -pppm command. Thus it can increase the cost of the -PPPM calculation if it is needed on a large fraction of the simulation -timesteps. -

    -

    Various fixes can contribute to the total potential energy of the -system. See the doc pages for individual fixes for -details. The thermo option of the -compute_modify command determines whether these -contributions are added into the computed potential energy. If no -keywords are specified the default is yes. If any keywords are -specified, the default is no. -

    -

    A compute of this style with the ID of "thermo_pe" is created when -LAMMPS starts up, as if this command were in the input script: -

    -
    compute thermo_pe all pe 
-
    -

    See the "thermo_style" command for more details. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the potential energy). This -value can be used by any command that uses a global scalar value from -a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "extensive". The -scalar value will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute pe/atom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_pe_atom.html b/doc/doc2/compute_pe_atom.html deleted file mode 100644 index 7138369832..0000000000 --- a/doc/doc2/compute_pe_atom.html +++ /dev/null @@ -1,97 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute pe/atom command -

    -

    Syntax: -

    -
    compute ID group-ID pe/atom keyword ... 
-
    -
    • ID, group-ID are documented in compute command -
    • pe/atom = style name of this compute command -
    • zero or more keywords may be appended -
    • keyword = pair or bond or angle or dihedral or improper or kspace -
    -

    Examples: -

    -
    compute 1 all pe/atom
-compute 1 all pe/atom pair
-compute 1 all pe/atom pair bond 
-
    -

    Description: -

    -

    Define a computation that computes the per-atom potential energy for -each atom in a group. See the compute pe command if -you want the potential energy of the entire system. -

    -

    The per-atom energy is calculated by the various pair, bond, etc -potentials defined for the simulation. If no extra keywords are -listed, then the potential energy is the sum of pair, bond, angle, -dihedral,improper, and kspace energy. If any extra keywords are -listed, then only those components are summed to compute the potential -energy. -

    -

    Note that the energy of each atom is due to its interaction with all -other atoms in the simulation, not just with other atoms in the group. -

    -

    For an energy contribution produced by a small set of atoms (e.g. 4 -atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that -energy is assigned in equal portions to each atom in the set. -E.g. 1/4 of the dihedral energy to each of the 4 atoms. -

    -

    The dihedral_style charmm style calculates -pairwise interactions between 1-4 atoms. The energy contribution of -these terms is included in the pair energy, not the dihedral energy. -

    -

    The KSpace contribution is calculated using the method in -(Heyes) for the Ewald method and a related method for PPPM, -as specified by the kspace_style pppm command. -For PPPM, the calcluation requires 1 extra FFT each timestep that -per-atom energy is calculated. Thie document -describes how the long-range per-atom energy calculation is performed. -

    -

    As an example of per-atom potential energy compared to total potential -energy, these lines in an input script should yield the same result -in the last 2 columns of thermo output: -

    -
    compute		peratom all pe/atom
-compute		pe all reduce sum c_peratom
-thermo_style	custom step temp etotal press pe c_pe 
-
    -

    IMPORTANT NOTE: The per-atom energy does not any Lennard-Jones tail -corrections invoked by the pair_modify tail yes -command, since those are global contributions to the system energy. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-atom vector values will be in energy units. -

    -

    Restrictions: -

    -

    Related commands: -

    -

    compute pe, compute -stress/atom -

    -

    Default: none -

    -
    - - - -

    (Heyes) Heyes, Phys Rev B 49, 755 (1994), -

    - diff --git a/doc/doc2/compute_plasticity_atom.html b/doc/doc2/compute_plasticity_atom.html deleted file mode 100644 index ea39315d00..0000000000 --- a/doc/doc2/compute_plasticity_atom.html +++ /dev/null @@ -1,73 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute plasticity/atom command -

    -

    Syntax: -

    -
    compute ID group-ID plasticity/atom 
-
    -
    • ID, group-ID are documented in compute command -
    • plasticity/atom = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all plasticity/atom 
-
    -

    Description: -

    -

    Define a computation that calculates the per-atom plasticity for each -atom in a group. This is a quantity relevant for Peridynamics -models. See this document -for an overview of LAMMPS commands for Peridynamics modeling. -

    -

    The plasticity for a Peridynamic particle is the so-called consistency -parameter (lambda). For elastic deformation lambda = 0, otherwise -lambda > 0 for plastic deformation. For details, see -(Mitchell) and the PDF doc included in the LAMMPS -distro in doc/PDF/PDLammps_EPS.pdf. -

    -

    This command can be invoked for one of the Peridynamic pair -styles: peri/eps. -

    -

    The plasticity value will be 0.0 for atoms not in the specified -compute group. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of LAMMPS output options. -

    -

    The per-atom vector values are unitlesss numbers (lambda) >= 0.0. -

    -

    Restrictions: -

    -

    This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute damage, compute -dilatation -

    -

    Default: none -

    -
    - - - -

    (Mitchell) Mitchell, "A non-local, ordinary-state-based -viscoelasticity model for peridynamics", Sandia National Lab Report, -8064:1-28 (2011). -

    - diff --git a/doc/doc2/compute_pressure.html b/doc/doc2/compute_pressure.html deleted file mode 100644 index c284043fef..0000000000 --- a/doc/doc2/compute_pressure.html +++ /dev/null @@ -1,155 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute pressure command -

    -

    compute pressure/cuda command -

    -

    Syntax: -

    -
    compute ID group-ID pressure temp-ID keyword ... 
-
    -
    • ID, group-ID are documented in compute command -
    • pressure = style name of this compute command -
    • temp-ID = ID of compute that calculates temperature, can be NULL if not needed -
    • zero or more keywords may be appended -
    • keyword = ke or pair or bond or angle or dihedral or improper or kspace or fix or virial -
    -

    Examples: -

    -
    compute 1 all pressure thermo_temp
-compute 1 all pressure NULL pair bond 
-
    -

    Description: -

    -

    Define a computation that calculates the pressure of the entire system -of atoms. The specified group must be "all". See the compute -stress/atom command if you want per-atom -pressure (stress). These per-atom values could be summed for a group -of atoms via the compute reduce command. -

    -

    The pressure is computed by the formula -

    -
    -
    -

    where N is the number of atoms in the system (see discussion of DOF -below), Kb is the Boltzmann constant, T is the temperature, d is the -dimensionality of the system (2 or 3 for 2d/3d), V is the system -volume (or area in 2d), and the second term is the virial, computed -within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body, -and long-range interactions. Fixes that impose constraints -(e.g. the fix shake command) also contribute to the -virial term. -

    -

    A symmetric pressure tensor, stored as a 6-element vector, is also -calculated by this compute. The 6 components of the vector are -ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components -(where I and J = x,y,z) is similar to the above formula, except that -the first term uses components of the kinetic energy tensor and the -second term uses components of the virial tensor: -

    -
    -
    -

    If no extra keywords are listed, the entire equations above are -calculated. This includes a kinetic energy (temperature) term and the -virial as the sum of pair, bond, angle, dihedral, improper, kspace -(long-range), and fix contributions to the force on each atom. If any -extra keywords are listed, then only those components are summed to -compute temperature or ke and/or the virial. The virial keyword -means include all terms except the kinetic energy ke. -

    -

    Details of how LAMMPS computes the virial efficiently for the entire -system, including the effects of periodic boundary conditions is -discussed in (Thompson). -

    -

    The temperature and kinetic energy tensor is not calculated by this -compute, but rather by the temperature compute specified with the -command. If the kinetic energy is not included in the pressure, than -the temperature compute is not used and can be specified as NULL. -Normally the temperature compute used by compute pressure should -calculate the temperature of all atoms for consistency with the virial -term, but any compute style that calculates temperature can be used, -e.g. one that excludes frozen atoms or other degrees of freedom. -

    -

    Note that if desired the specified temperature compute can be one that -subtracts off a bias to calculate a temperature using only the thermal -velocity of the atoms, e.g. by subtracting a background streaming -velocity. See the doc pages for individual compute -commands to determine which ones include a bias. -

    -

    Also note that the N in the first formula above is really -degrees-of-freedom divided by d = dimensionality, where the DOF value -is calcluated by the temperature compute. See the various compute -temperature styles for details. -

    -

    A compute of this style with the ID of "thermo_press" is created when -LAMMPS starts up, as if this command were in the input script: -

    -
    compute thermo_press all pressure thermo_temp 
-
    -

    where "thermo_temp" is the ID of a similarly defined compute of style -"temp". See the "thermo_style" command for more details. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the pressure) and a global -vector of length 6 (pressure tensor), which can be accessed by indices -1-6. These values can be used by any command that uses global scalar -or vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar and vector values calculated by this compute are -"intensive". The scalar and vector values will be in pressure -units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp, compute -stress/atom, -thermo_style, -

    -

    Default: none -

    -
    - - - -

    (Thompson) Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). -

    - diff --git a/doc/doc2/compute_property_atom.html b/doc/doc2/compute_property_atom.html deleted file mode 100644 index ca449ada49..0000000000 --- a/doc/doc2/compute_property_atom.html +++ /dev/null @@ -1,173 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute property/atom command -

    -

    Syntax: -

    -
    compute ID group-ID property/atom input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • property/atom = style name of this compute command - -
    • input = one or more atom attributes - -
        possible attributes = id, mol, proc, type, mass,
- 	                x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-		        vx, vy, vz, fx, fy, fz,
-                        q, mux, muy, muz, mu,
-                        radius, diameter, omegax, omegay, omegaz,
-			angmomx, angmomy, angmomz,
-			shapex,shapey, shapez,
-		        quatw, quati, quatj, quatk, tqx, tqy, tqz,
-			end1x, end1y, end1z, end2x, end2y, end2z,
-			corner1x, corner1y, corner1z,
-			corner2x, corner2y, corner2z,
-			corner3x, corner3y, corner3z,
-			nbonds,
-                        vfrac, s0,
-			spin, eradius, ervel, erforce,
-                        rho, drho, e, de, cv,
-                        i_name, d_name 
-
      -
            id = atom ID
-      mol = molecule ID
-      proc = ID of processor that owns atom
-      type = atom type
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipole moment of atom
-      mu = magnitude of dipole moment of atom
-      radius,diameter = radius,diameter of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      shapex,shapey,shapez = 3 diameters of aspherical particle
-      quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
-      tqx,tqy,tqz = torque on finite-size particles
-      end12x, end12y, end12z = end points of line segment
-      corner123x, corner123y, corner123z = corner points of triangle
-      nbonds = number of bonds assigned to an atom 
-
      -
            PERI package per-atom properties:
-      vfrac = ???
-      s0 = ??? 
-
      -
            USER-EFF and USER-AWPMD package per-atom properties:
-      spin = electron spin
-      eradius = electron radius
-      ervel = electron radial velocity
-      erforce = electron radial force 
-
      -
            USER-SPH package per-atom properties:
-      rho = ???
-      drho = ???
-      e = ???
-      de = ???
-      cv = ??? 
-
      -
            fix property/atom per-atom properties:
-      i_name = custom integer vector with name
-      d_name = custom integer vector with name 
-
      - -
    -

    Examples: -

    -
    compute 1 all property/atom xs vx fx mux 
-compute 2 all property/atom type
-compute 1 all property/atom ix iy iz 
-
    -

    Description: -

    -

    Define a computation that simply stores atom attributes for each atom -in the group. This is useful so that the values can be used by other -output commands that take computes as -inputs. See for example, the compute reduce, -fix ave/atom, fix ave/histo, -fix ave/spatial, and atom-style -variable commands. -

    -

    The list of possible attributes is the same as that used by the dump -custom command, which describes their meaning, with some -additional quantities that are only defined for certain atom -styles. Basically, this augmented list gives an -input script access to any per-atom quantity stored by LAMMPS. -

    -

    The values are stored in a per-atom vector or array as discussed -below. Zeroes are stored for atoms not in the specified group or for -quantities that are not defined for a particular particle in the group -(e.g. shapex if the particle is not an ellipsoid). -

    -

    The additional quantities only accessible via this command, and not -directly via the dump custom command, are as follows. -

    -

    Shapex, shapey, and shapez are defined for ellipsoidal particles -and define the 3d shape of each particle. -

    -

    Quatw, quati, quatj, and quatk are defined for ellipsoidal -particles and body particles and store the 4-vector quaternion -representing the orientation of each particle. See the set -command for an explanation of the quaternion vector. -

    -

    End1x, end1y, end1z, end2x, end2y, end2z, are defined for -line segment particles and define the end points of each line segment. -

    -

    Corner1x, corner1y, corner1z, corner2x, corner2y, -corner2z, corner3x, corner3y, corner3z, are defined for -triangular particles and define the corner points of each triangle. -

    -

    Nbonds is available for all molecular atom styles and refers to the -number of explicit bonds assigned to an atom. Note that if the -newton bond command is set to on, which is the -default, then every bond in the system is assigned to only one of the -two atoms in the bond. Thus a bond between atoms I,J may be tallied -for either atom I or atom J. If newton bond off is set, -it will be tallied with both atom I and atom J. -

    -

    The i_name and d_name attributes refer to custom integer and -floating-point properties that have been added to each atom via the -fix property/atom command. When that command -is used specific names are given to each attribute which are what is -specified as the "name" portion of i_name or d_name. -

    -

    Output info: -

    -

    This compute calculates a per-atom vector or per-atom array depending -on the number of input values. If a single input is specified, a -per-atom vector is produced. If two or more inputs are specified, a -per-atom array is produced where the number of columns = the number of -inputs. The vector or array can be accessed by any command that uses -per-atom values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector or array values will be in whatever units the -corresponding attribute is in, e.g. velocity units for vx, charge -units for q, etc. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump custom, compute reduce, fix -ave/atom, fix ave/spatial, -fix property/atom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_property_chunk.html b/doc/doc2/compute_property_chunk.html deleted file mode 100644 index cf4cc03019..0000000000 --- a/doc/doc2/compute_property_chunk.html +++ /dev/null @@ -1,127 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute property/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID property/chunk chunkID input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • property/chunk = style name of this compute command - -
    • input = one or more attributes - -
        attributes = count, id, coord1, coord2, coord3
-    count = # of atoms in chunk 
-    id = original chunk IDs before compression by compute chunk/atom
-    coord123 = coordinates for spatial bins calculated by compute chunk/atom 
-
      - -
    -

    Examples: -

    -
    compute 1 all property/chunk count
-compute 1 all property/chunk ID coord1 
-
    -

    Description: -

    -

    Define a computation that stores the specified attributes of chunks of -atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates and stores the specified attributes of chunks -as global data so they can be accessed by other output -commands and used in conjunction with -other commands that generate per-chunk data, such as compute -com/chunk or compute -msd/chunk. -

    -

    Note that only atoms in the specified group contribute to the -calculation of the count attribute. The compute -chunk/atom command defines its own group; -atoms will have a chunk ID = 0 if they are not in that group, -signifying they are not assigned to a chunk, and will thus also not -contribute to this calculation. You can specify the "all" group for -this command if you simply want to include atoms with non-zero chunk -IDs. -

    -

    The count attribute is the number of atoms in the chunk. -

    -

    The id attribute stores the original chunk ID for each chunk. It -can only be used if the compress keyword was set to yes for the -compute chunk/atom command referenced by -chunkID. This means that the original chunk IDs (e.g. molecule IDs) -will have been compressed to remove chunk IDs with no atoms assigned -to them. Thus a compresed chunk ID of 3 may correspond to an original -chunk ID (molecule ID in this case) of 415. The id attribute will -then be 415 for the 3rd chunk. -

    -

    The coordN attributes can only be used if a binning style was used -in the compute chunk/atom command referenced -by chunkID. For bin/1d, bin/2d, and bin/3d styles the attribute -is the center point of the bin in the corresponding dimension. Style -bin/1d only defines a coord1 attribute. Style bin/2d adds a -coord2 attribute. Style bin/3d adds a coord3 attribute. -

    -

    Note that if the value of the units keyword used in the compute -chunk/atom command is box or lattice, the -coordN attributes will be in distance units. If the -value of the units keyword is reduced, the coordN attributes -will be in unitless reduced units (0-1). -

    -

    The simplest way to output the results of the compute property/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk1 all property/chunk cc1
-compute myChunk2 all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global vector or global array depending on -the number of input values. The length of the vector or number of -rows in the array is the number of chunks. -

    -

    This compute calculates a global vector or global array where the -number of rows = the number of chunks Nchunk as calculated by the -specified compute chunk/atom command. If a -single input is specified, a global vector is produced. If two or -more inputs are specified, a global array is produced where the number -of columns = the number of inputs. The vector or array can be -accessed by any command that uses global values from a compute as -input. See this section for an overview -of LAMMPS output options. -

    -

    The vector or array values are "intensive". The values will be -unitless or in the units discussed above. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix ave/chunk -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_property_local.html b/doc/doc2/compute_property_local.html deleted file mode 100644 index 440fa21fe2..0000000000 --- a/doc/doc2/compute_property_local.html +++ /dev/null @@ -1,151 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute property/local command -

    -

    Syntax: -

    -
    compute ID group-ID property/local input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • property/local = style name of this compute command - -
    • input = one or more attributes - -
        possible attributes = natom1 natom2 ntype1 ntype2
-		        patom1 patom2 ptype1 ptype2
-                        batom1 batom2 btype
-                        aatom1 aatom2 aatom3 atype
-                        datom1 datom2 datom3 dtype
-                        iatom1 iatom2 iatom3 itype 
-
      -
           natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
-     ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
-     patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
-     ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
-     batom1, batom2 = IDs of 2 atoms in each bond
-     btype = bond type of each bond
-     aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
-     atype = angle type of each angle
-     datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
-     dtype = dihedral type of each dihedral
-     iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
-     itype = improper type of each improper 
-
      - -
    -

    Examples: -

    -
    compute 1 all property/local btype batom1 batom2
-compute 1 all property/local atype aatom2 
-
    -

    Description: -

    -

    Define a computation that stores the specified attributes as local -data so it can be accessed by other output -commands. If the input attributes refer -to bond information, then the number of datums generated, aggregated -across all processors, equals the number of bonds in the system. -Ditto for pairs, angles, etc. -

    -

    If multiple input attributes are specified then they must all generate -the same amount of information, so that the resulting local array has -the same number of rows for each column. This means that only bond -attributes can be specified together, or angle attributes, etc. Bond -and angle attributes can not be mixed in the same compute -property/local command. -

    -

    If the inputs are pair attributes, the local data is generated by -looping over the pairwise neighbor list. Info about an individual -pairwise interaction will only be included if both atoms in the pair -are in the specified compute group. For natom1 and natom2, all -atom pairs in the neighbor list are considered (out to the neighbor -cutoff = force cutoff + neighbor skin). For patom1 -and patom2, the distance between the atoms must be less than the -force cutoff distance for that pair to be included, as defined by the -pair_style and pair_coeff -commands. -

    -

    If the inputs are bond, angle, etc attributes, the local data is -generated by looping over all the atoms owned on a processor and -extracting bond, angle, etc info. For bonds, info about an individual -bond will only be included if both atoms in the bond are in the -specified compute group. Likewise for angles, dihedrals, etc. -

    -

    For bonds and angles, a bonds/angles that have been broken by setting -their bond/angle type to 0 will not be included. Bonds/angles that -have been turned off (see the fix shake or -delete_bonds commands) by setting their bond/angle -type negative are written into the file. This is consistent with the -compute bond/local and compute -angle/local commands -

    -

    Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, output from the compute -bond/local command can be combined with bond -atom indices from this command and output by the dump -local command in a consistent way. -

    -

    The natom1 and natom2, or patom1 and patom2 attributes refer -to the atom IDs of the 2 atoms in each pairwise interaction computed -by the pair_style command. The ntype1 and -ntype2, or ptype1 and ptype2 attributes refer to the atom types -of the 2 atoms in each pairwise interaction. -

    -

    IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, -1-4 interactions within the molecular topology, their pairwise -interaction may be turned off, and thus they may not appear in the -neighbor list, and will not be part of the local data created by this -command. More specifically, this may be true of I,J pairs with a -weighting factor of 0.0; pairs with a non-zero weighting factor are -included. The weighting factors for 1-2, 1-3, and 1-4 pairwise -interactions are set by the special_bonds -command. -

    -

    The batom1 and batom2 attributes refer to the atom IDs of the 2 -atoms in each bond. The btype attribute refers to -the type of the bond, from 1 to Nbtypes = # of bond types. The number -of bond types is defined in the data file read by the -read_data command. -

    -

    The attributes that start with "a", "d", "i", refer to similar values -for angles, dihedrals, and -impropers. -

    -

    Output info: -

    -

    This compute calculates a local vector or local array depending on the -number of input values. The length of the vector or number of rows in -the array is the number of bonds, angles, etc. If a single input is -specified, a local vector is produced. If two or more inputs are -specified, a local array is produced where the number of columns = the -number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector or array values will be integers that correspond to the -specified attribute. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump local, compute reduce -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_rdf.html b/doc/doc2/compute_rdf.html deleted file mode 100644 index e711008099..0000000000 --- a/doc/doc2/compute_rdf.html +++ /dev/null @@ -1,160 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute rdf command -

    -

    Syntax: -

    -
    compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... 
-
    -
    • ID, group-ID are documented in compute command -
    • rdf = style name of this compute command -
    • Nbin = number of RDF bins -
    • itypeN = central atom type for Nth RDF histogram (see asterisk form below) -
    • jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) -
    -

    Examples: -

    -
    compute 1 all rdf 100
-compute 1 all rdf 100 1 1
-compute 1 all rdf 100 * 3
-compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
-compute 1 fluid rdf 500 1*3 2 5 *10 
-
    -

    Description: -

    -

    Define a computation that calculates the radial distribution function -(RDF), also called g(r), and the coordination number for a group of -particles. Both are calculated in histogram form by binning pairwise -distances into Nbin bins from 0.0 to the maximum force cutoff -defined by the pair_style command. The bins are of -uniform size in radial distance. Thus a single bin encompasses a thin -shell of distances in 3d and a thin ring of distances in 2d. -

    -

    IMPORTANT NOTE: If you have a bonded system, then the settings of -special_bonds command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the special_bonds -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the RDF. This does not apply when -using long-range coulomb (coul/long, coul/msm, coul/wolf or similar. -One way to get around this would be to set special_bond scaling factors -to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another -workaround is to write a dump file, and use the rerun command -to compute the RDF for snapshots in the dump file. The rerun script -can use a special_bonds command that includes all -pairs in the neighbor list. -

    -

    The itypeN and jtypeN arguments are optional. These arguments -must come in pairs. If no pairs are listed, then a single histogram -is computed for g(r) between all atom types. If one or more pairs are -listed, then a separate histogram is generated for each -itype,jtype pair. -

    -

    The itypeN and jtypeN settings can be specified in one of two -ways. An explicit numeric value can be used, as in the 4th example -above. Or a wild-card asterisk can be used to specify a range of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). -

    -

    If both itypeN and jtypeN are single values, as in the 4th example -above, this means that a g(r) is computed where atoms of type itypeN -are the central atom, and atoms of type jtypeN are the distribution -atom. If either itypeN and jtypeN represent a range of values via -the wild-card asterisk, as in the 5th example above, this means that a -g(r) is computed where atoms of any of the range of types represented -by itypeN are the central atom, and atoms of any of the range of -types represented by jtypeN are the distribution atom. -

    -

    Pairwise distances are generated by looping over a pairwise neighbor -list, just as they would be in a pair_style -computation. The distance between two atoms I and J is included in a -specific histogram if the following criteria are met: -

    -
    • atoms I,J are both in the specified compute group -
    • the distance between atoms I,J is less than the maximum force cutoff -
    • the type of the I atom matches itypeN (one or a range of types) -
    • the type of the J atom matches jtypeN (one or a range of types) -
    -

    It is OK if a particular pairwise distance is included in more than -one individual histogram, due to the way the itypeN and jtypeN -arguments are specified. -

    -

    The g(r) value for a bin is calculated from the histogram count by -scaling it by the idealized number of how many counts there would be -if atoms of type jtypeN were uniformly distributed. Thus it -involves the count of itypeN atoms, the count of jtypeN atoms, the -volume of the entire simulation box, and the volume of the bin's thin -shell in 3d (or the area of the bin's thin ring in 2d). -

    -

    A coordination number coord(r) is also calculated, which is the number -of atoms of type jtypeN within the current bin or closer, averaged -over atoms of type itypeN. This is calculated as the area- or -volume-weighted sum of g(r) values over all bins up to and including -the current bin, multiplied by the global average volume density of -atoms of type jtypeN. -

    -

    The simplest way to output the results of the compute rdf calculation -to a file is to use the fix ave/time command, for -example: -

    -
    compute myRDF all rdf 50
-fix 1 all ave/time 100 1 100 c_myRDF file tmp.rdf mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array with the number of rows = -Nbins, and the number of columns = 1 + 2*Npairs, where Npairs is the -number of I,J pairings specified. The first column has the bin -coordinate (center of the bin), Each successive set of 2 columns has -the g(r) and coord(r) values for a specific set of itypeN versus -jtypeN interactions, as described above. These values can be used -by any command that uses a global values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The array values calculated by this compute are all "intensive". -

    -

    The first column of array values will be in distance -units. The g(r) columns of array values are normalized -numbers >= 0.0. The coordination number columns of array values are -also numbers >= 0.0. -

    -

    Restrictions: -

    -

    The RDF is not computed for distances longer than the force cutoff, -since processors (in parallel) don't know about atom coordinates for -atoms further away than that distance. If you want an RDF for larger -distances, you can use the rerun command to post-process -a dump file and set the cutoff for the potential to be longer in the -rerun script. Note that in the rerun context, the force cutoff is -arbitrary, since you aren't running dynamics and thus are not changing -your model. The definition of g(r) used by LAMMPS is only appropriate -for characterizing atoms that are uniformly distributed throughout the -simulation cell. In such cases, the coordination number is still -correct and meaningful. As an example, if a large simulation cell -contains only one atom of type itypeN and one of jtypeN, then g(r) -will register an arbitrarily large spike at whatever distance they -happen to be at, and zero everywhere else. Coord(r) will show a step -change from zero to one at the location of the spike in g(r). -

    -

    Related commands: -

    -

    fix ave/time -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_reduce.html b/doc/doc2/compute_reduce.html deleted file mode 100644 index ce267fe4e5..0000000000 --- a/doc/doc2/compute_reduce.html +++ /dev/null @@ -1,200 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute reduce command -

    -

    compute reduce/region command -

    -

    Syntax: -

    -
    compute ID group-ID style arg mode input1 input2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • style = reduce or reduce/region - -
        reduce arg = none
-  reduce/region arg = region-ID
-    region-ID = ID of region to use for choosing atoms 
-
      -
    • mode = sum or min or max or ave or sumsq or avesq - -
    • one or more inputs can be listed - -
    • input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name - -
        x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = per-atom or local vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
-  f_ID = per-atom or local vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name 
-
      -
    • zero or more keyword/args pairs may be appended - -
    • keyword = replace - -
        replace args = vec1 vec2
-    vec1 = reduced value from this input vector will be replaced
-    vec2 = replace it with vec1[N] where N is index of max/min value from vec2 
-
      - -
    -

    Examples: -

    -
    compute 1 all reduce sum c_force
-compute 1 all reduce/region subbox sum c_force
-compute 2 all reduce min c_press[2] f_ave v_myKE
-compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3 
-
    -

    Description: -

    -

    Define a calculation that "reduces" one or more vector inputs into -scalar values, one per listed input. The inputs can be per-atom or -local quantities; they cannot be global quantities. Atom attributes -are per-atom quantities, computes and fixes -may generate any of the three kinds of quantities, and atom-style -variables generate per-atom quantities. See the -variable command and its special functions which can -perform the same operations as the compute reduce command on global -vectors. -

    -

    The reduction operation is specified by the mode setting. The sum -option adds the values in the vector into a global total. The min -or max options find the minimum or maximum value across all vector -values. The ave setting adds the vector values into a global total, -then divides by the number of values in the vector. The sumsq -option sums the square of the values in the vector into a global -total. The avesq setting does the same as sumsq, then divdes the -sum of squares by the number of values. The last two options can be -useful for calculating the variance of some quantity, e.g. variance = -sumsq - ave^2. -

    -

    Each listed input is operated on independently. For per-atom inputs, -the group specified with this command means only atoms within the -group contribute to the result. For per-atom inputs, if the compute -reduce/region command is used, the atoms must also currently be within -the region. Note that an input that produces per-atom quantities may -define its own group which affects the quantities it returns. For -example, if a compute is used as an input which generates a per-atom -vector, it will generate values of 0.0 for atoms that are not in the -group specified for that compute. -

    -

    Each listed input can be an atom attribute (position, velocity, force -component) or can be the result of a compute or -fix or the evaluation of an atom-style -variable. -

    -

    The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are -self-explanatory. Note that other atom attributes can be used as -inputs to this fix by using the compute -property/atom command and then specifying -an input value from that compute. -

    -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. Computes can generate -per-atom or local quantities. See the individual -compute doc page for details. If no bracketed integer -is appended, the vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the array calculated -by the compute is used. Users can also write code for their own -compute styles and add them to LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. Fixes can generate per-atom -or local quantities. See the individual fix doc page for -details. Note that some fixes only produce their values on certain -timesteps, which must be compatible with when compute reduce -references the values, else an error results. If no bracketed integer -is appended, the vector calculated by the fix is used. If a bracketed -integer is appended, the Ith column of the array calculated by the fix -is used. Users can also write code for their own fix style and add -them to LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. It must be an -atom-style variable. Atom-style variables can -reference thermodynamic keywords and various per-atom attributes, or -invoke other computes, fixes, or variables when they are evaluated, so -this is a very general means of generating per-atom quantities to -reduce. -

    -
    - -

    If the replace keyword is used, two indices vec1 and vec2 are -specified, where each index ranges from 1 to the # of input values. -The replace keyword can only be used if the mode is min or max. -It works as follows. A min/max is computed as usual on the vec2 -input vector. The index N of that value within vec2 is also stored. -Then, instead of performing a min/max on the vec1 input vector, the -stored index is used to select the Nth element of the vec1 vector. -

    -

    Thus, for example, if you wish to use this compute to find the bond -with maximum stretch, you can do it as follows: -

    -
    compute 1 all property/local batom1 batom2
-compute	2 all bond/local dist
-compute	3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
-thermo_style custom step temp c_3[1] c_3[2] c_3[3] 
-
    -

    The first two input values in the compute reduce command are vectors -with the IDs of the 2 atoms in each bond, using the compute -property/local command. The last input -value is bond distance, using the compute -bond/local command. Instead of taking the -max of the two atom ID vectors, which does not yield useful -information in this context, the replace keywords will extract the -atom IDs for the two atoms in the bond of maximum stretch. These atom -IDs and the bond stretch will be printed with thermodynamic output. -

    -
    - -

    If a single input is specified this compute produces a global scalar -value. If multiple inputs are specified, this compute produces a -global vector of values, the length of which is equal to the number of -inputs specified. -

    -

    As discussed below, for the sum and sumsq modes, the value(s) -produced by this compute are all "extensive", meaning their value -scales linearly with the number of atoms involved. If normalized -values are desired, this compute can be accessed by the thermo_style -custom command with thermo_modify norm -yes set as an option. Or it can be accessed by a -variable that divides by the appropriate atom count. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar if a single input value is -specified or a global vector of length N where N is the number of -inputs, and which can be accessed by indices 1 to N. These values can -be used by any command that uses global scalar or vector values from a -compute as input. See Section_howto 15 -for an overview of LAMMPS output options. -

    -

    All the scalar or vector values calculated by this compute are -"intensive", except when the sum or sumsq modes are used on -per-atom or local vectors, in which case the calculated values are -"extensive". -

    -

    The scalar or vector values will be in whatever units the -quantities being reduced are in. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute, fix, variable -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_saed.html b/doc/doc2/compute_saed.html deleted file mode 100644 index c99d3ae823..0000000000 --- a/doc/doc2/compute_saed.html +++ /dev/null @@ -1,191 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute saed command -

    -

    Syntax: -

    -
    compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • saed = style name of this compute command - -
    • lambda = wavelength of incident radiation (length units) - -
    • type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = Kmax or Zone or dR_Ewald or c or manual or echo - -
        Kmax value = Maximum distance explored from reciprocal space origin 
-                 (inverse length units)
-  Zone values = z1 z2 z3
-    z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all 
-               reciprocal space will be meshed up to Kmax
-  dR_Ewald value = Thickness of Ewald sphere slice intercepting 
-                     reciprocal space (inverse length units)
-  c values = c1 c2 c3
-    c1,c2,c3 = parameters to adjust the spacing of the reciprocal 
-               lattice nodes in the h, k, and l directions respectively
-  manual = flag to use manual spacing of reciprocal lattice points   
-             based on the values of the c parameters 
-  echo = flag to provide extra output for debugging purposes 
-
      - -
    -

    Examples: -

    -
    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
-compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo 
-
    -
    fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed 
-
    -

    Description: -

    -

    Define a computation that calculates electron diffraction intensity as -described in (Coleman) on a mesh of reciprocal lattice nodes -defined by the entire simulation domain (or manually) using simulated -radiation of wavelength lambda. -

    -

    The electron diffraction intensity I at each reciprocal lattice point -is computed from the structure factor F using the equations: -

    -
    -
    -
    -
    -

    Here, K is the location of the reciprocal lattice node, rj is the -position of each atom, fj are atomic scattering factors. -

    -

    Diffraction intensities are calculated on a three-dimensional mesh of -reciprocal lattice nodes. The mesh spacing is defined either (a) by -the entire simulation domain or (b) manually using selected values as -shown in the 2D diagram below. -

    -
    -
    -

    For a mesh defined by the simulation domain, a rectilinear grid is -constructed with spacing c*inv(A) along each reciprocal lattice -axis. Where A are the vectors corresponding to the edges of the -simulation cell. If one or two directions has non-periodic boundary -conditions, then the spacing in these directions is defined from the -average of the (inversed) box lengths with periodic boundary conditions. -Meshes defined by the simulation domain must contain at least one periodic -boundary. -

    -

    If the manual flag is included, the mesh of reciprocal lattice nodes -will defined using the c values for the spacing along each reciprocal -lattice axis. Note that manual mapping of the reciprocal space mesh is -good for comparing diffraction results from multiple simulations; however -it can reduce the likelihood that Bragg reflections will be satisfied -unless small spacing parameters <0.05 Angstrom^(-1) are implemented. -Meshes with manual spacing do not require a periodic boundary. -

    -

    The limits of the reciprocal lattice mesh are determined by the use of -the Kmax, Zone, and dR_Ewald parameters. The rectilinear mesh -created about the origin of reciprocal space is terminated at the -boundary of a sphere of radius Kmax centered at the origin. If -Zone parameters z1=z2=z3=0 are used, diffraction intensities are -computed throughout the entire spherical volume - note this can greatly -increase the cost of computation. Otherwise, Zone parameters will -denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an -intersecting Ewald sphere. Diffraction intensities will only be -computed at the intersection of the reciprocal lattice mesh and a -dR_Ewald thick surface of the Ewald sphere. See the example 3D -intestiety data and the intersection of a [010] zone axis in the below image. -

    -
    -
    -

    The atomic scattering factors, fj, accounts for the reduction in -diffraction intensity due to Compton scattering. Compute saed uses -analytical approximations of the atomic scattering factors that vary -for each atom type (type1 type2 ... typeN) and angle of diffraction. -The analytic approximation is computed using the formula -(Brown): -

    -
    -
    -

    Coefficients parameterized by (Fox) are assigned for each -atom type designating the chemical symbol and charge of each atom -type. Valid chemical symbols for compute saed are: -

    -

    H: He: Li: Be: B: - C: N: O: F: Ne: - Na: Mg: Al: Si: P: - S: Cl: Ar: K: Ca: - Sc: Ti: V: Cr: Mn: - Fe: Co: Ni: Cu: Zn: - Ga: Ge: As: Se: Br: - Kr: Rb: Sr: Y: Zr: - Nb: Mo: Tc: Ru: Rh: - Pd: Ag: Cd: In: Sn: - Sb: Te: I: Xe: Cs: - Ba: La: Ce: Pr: Nd: - Pm: Sm: Eu: Gd: Tb: - Dy: Ho: Er: Tm: Yb: - Lu: Hf: Ta: W: Re: - Os: Ir: Pt: Au: Hg: - Tl: Pb: Bi: Po: At: - Rn: Fr: Ra: Ac: Th: - Pa: U: Np: Pu: Am: - Cm: Bk: Cf:tb(c=5,s=:) -

    -

    If the echo keyword is specified, compute saed will provide extra -reporting information to the screen. -

    -

    Output info: -

    -

    This compute calculates a global vector. The length of the vector is -the number of reciprocal lattice nodes that are explored by the mesh. -The entries of the global vector are the computed diffraction -intensities as described above. -

    -

    The vector can be accessed by any command that uses global values -from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    All array values calculated by this compute are "intensive". -

    -

    Restrictions: -

    -

    The compute_saed command does not work for triclinic cells. -

    -

    Related commands: -

    -

    fix saed_vtk, compute xrd -

    -

    Default: -

    -

    The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = -0.01. -

    -
    - - - -

    (Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 -(2013). -

    - - -

    (Brown) Brown et al. International Tables for Crystallography -Volume C: Mathematical and Chemical Tables, 554-95 (2004). -

    - - -

    (Fox) Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 -(1989). -

    - diff --git a/doc/doc2/compute_slice.html b/doc/doc2/compute_slice.html deleted file mode 100644 index e4f82a1652..0000000000 --- a/doc/doc2/compute_slice.html +++ /dev/null @@ -1,124 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute slice command -

    -

    Syntax: -

    -
    compute ID group-ID slice Nstart Nstop Nskip input1 input2 ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • slice = style name of this compute command - -
    • Nstart = starting index within input vector(s) - -
    • Nstop = stopping index within input vector(s) - -
    • Nskip = extract every Nskip elements from input vector(s) - -
    • input = c_ID, c_ID[N], f_ID, f_ID[N] - -
        c_ID = global vector calculated by a compute with ID
-  c_ID[I] = Ith column of global array calculated by a compute with ID
-  f_ID = global vector calculated by a fix with ID
-  f_ID[I] = Ith column of global array calculated by a fix with ID 
-
      - -
    -

    Examples: -

    -
    compute 1 all slice 1 100 10 c_msdmol[4]
-compute 1 all slice 301 400 1 c_msdmol[4] 
-
    -

    Description: -

    -

    Define a calculation that "slices" one or more vector inputs into -smaller vectors, one per listed input. The inputs can be global -quantities; they cannot be per-atom or local quantities. -Computes and fixes may generate any of the -three kinds of quantities. Variables do not generate -global vectors. The group specified with this command is ignored. -

    -

    The values extracted from the input vector(s) are determined by the -Nstart, Nstop, and Nskip parameters. The elements of an input -vector of length N are indexed from 1 to N. Starting at element -Nstart, every Mth element is extracted, where M = Nskip, until -element Nstop is reached. The extracted quantities are stored as a -vector, which is typically shorter than the input vector. -

    -

    Each listed input is operated on independently to produce one output -vector. Each listed input must be a global vector or column of a -global array calculated by another compute or -fix. -

    -

    If an input value begins with "c_", a compute ID must follow which has -been previously defined in the input script and which generates a -global vector or array. See the individual compute doc -page for details. If no bracketed integer is appended, the vector -calculated by the compute is used. If a bracketed integer is -appended, the Ith column of the array calculated by the compute is -used. Users can also write code for their own compute styles and add -them to LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script and which generates a global -vector or array. See the individual fix doc page for -details. Note that some fixes only produce their values on certain -timesteps, which must be compatible with when compute slice references -the values, else an error results. If no bracketed integer is -appended, the vector calculated by the fix is used. If a bracketed -integer is appended, the Ith column of the array calculated by the fix -is used. Users can also write code for their own fix style and add -them to LAMMPS. -

    -

    If a single input is specified this compute produces a global vector, -even if the length of the vector is 1. If multiple inputs are -specified, then a global array of values is produced, with the number -of columns equal to the number of inputs specified. -

    -
    - -

    Output info: -

    -

    This compute calculates a global vector if a single input value is -specified or a global array with N columns where N is the number of -inputs. The length of the vector or the number of rows in the array -is equal to the number of values extracted from each input vector. -These values can be used by any command that uses global vector or -array values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector or array values calculated by this compute are simply -copies of values generated by computes or fixes that are input vectors -to this compute. If there is a single input vector of intensive -and/or extensive values, then each value in the vector of values -calculated by this compute will be "intensive" or "extensive", -depending on the corresponding input value. If there are multiple -input vectors, and all the values in them are intensive, then the -array values calculated by this compute are "intensive". If there are -multiple input vectors, and any value in them is extensive, then the -array values calculated by this compute are "extensive". -

    -

    The vector or array values will be in whatever units the -input quantities are in. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute, fix, compute -reduce -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_contact_radius.html b/doc/doc2/compute_smd_contact_radius.html deleted file mode 100644 index e2c2881821..0000000000 --- a/doc/doc2/compute_smd_contact_radius.html +++ /dev/null @@ -1,58 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/contact_radius command -

    -

    Syntax: -

    -
    compute ID group-ID smd/contact_radius 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/contact_radius = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/contact_radius 
-
    -

    Description: -

    -

    Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other. -The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles, -e.g., smd/hertz and smd/tri_surface. -

    -

    See this PDF guide to using Smooth Mach Dynamics in -LAMMPS. -

    -

    The value of the contact radius will be 0.0 for particles not in the -specified compute group. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-particle vector values will be in distance units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    dump custom smd/hertz smd/tri_surface -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_damage.html b/doc/doc2/compute_smd_damage.html deleted file mode 100644 index f4b10c50b2..0000000000 --- a/doc/doc2/compute_smd_damage.html +++ /dev/null @@ -1,53 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/damage command -

    -

    Syntax: -

    -
    compute ID group-ID smd/damage 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/damage = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/damage 
-
    -

    Description: -

    -

    Define a computation that calculates the damage status of SPH particles -according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Output Info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle values are dimensionless an in the range of zero to one. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    smd/plastic_strain, smd/tlsph_stress -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_hourglass_error.html b/doc/doc2/compute_smd_hourglass_error.html deleted file mode 100644 index f77e3d40b7..0000000000 --- a/doc/doc2/compute_smd_hourglass_error.html +++ /dev/null @@ -1,61 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/hourglass_error command -

    -

    Syntax: -

    -
    compute ID group-ID smd/hourglass_error 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/hourglass_error = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/hourglass_error 
-
    -

    Description: -

    -

    Define a computation which outputs the error of the approximated -relative separation with respect to the actual relative separation of -the particles i and j. Ideally, if the deformation gradient is exact, -and there exists a unique mapping between all particles' positions -within the neighborhood of the central node and the deformation gradient, -the approximated relative separation will coincide with the actual relative -separation of the particles i and j in the deformed configuration. -This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Output Info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle vector values will are dimensionless. See units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    This quantity will be computed only for particles which interact with tlsph pair style. -

    -

    Related Commands: -

    -

    smd/tlsph_defgrad -

    -

    Default: -

    - diff --git a/doc/doc2/compute_smd_internal_energy.html b/doc/doc2/compute_smd_internal_energy.html deleted file mode 100644 index f7852089e5..0000000000 --- a/doc/doc2/compute_smd_internal_energy.html +++ /dev/null @@ -1,51 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/internal_energy command -

    -

    Syntax: -

    -
    compute ID group-ID smd/internal_energy 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/smd/internal_energy = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/internal_energy 
-
    -

    Description: -

    -

    Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Output Info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle vector values will be given in units of energy. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles. -

    -

    Related Commands: -

    -

    Default: -

    - diff --git a/doc/doc2/compute_smd_plastic_strain.html b/doc/doc2/compute_smd_plastic_strain.html deleted file mode 100644 index 0a776ee033..0000000000 --- a/doc/doc2/compute_smd_plastic_strain.html +++ /dev/null @@ -1,54 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/plastic_strain command -

    -

    Syntax: -

    -
    compute ID group-ID smd/plastic_strain 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/plastic_strain = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/plastic_strain 
-
    -

    Description: -

    -

    Define a computation that outputs the equivalent plastic strain per particle. -This command is only meaningful if a material model with plasticity is defined. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Output Info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle values will be given dimensionless. See units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles. -

    -

    Related commands: -

    -

    smd/plastic_strain_rate, smd/tlsph_strain_rate, -smd/tlsph_strain -

    -

    Default: none

    - diff --git a/doc/doc2/compute_smd_plastic_strain_rate.html b/doc/doc2/compute_smd_plastic_strain_rate.html deleted file mode 100644 index 243c5d7d2c..0000000000 --- a/doc/doc2/compute_smd_plastic_strain_rate.html +++ /dev/null @@ -1,54 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/plastic_strain_rate command -

    -

    Syntax: -

    -
    compute ID group-ID smd/plastic_strain_rate 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/plastic_strain_rate = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/plastic_strain_rate 
-
    -

    Description: -

    -

    Define a computation that outputs the time rate of the equivalent plastic strain. -This command is only meaningful if a material model with plasticity is defined. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Output Info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle values will be given in units of one over time. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles. -

    -

    Related commands: -

    -

    smd/plastic_strain, smd/tlsph_strain_rate, -smd/tlsph_strain -

    -

    Default: none

    - diff --git a/doc/doc2/compute_smd_rho.html b/doc/doc2/compute_smd_rho.html deleted file mode 100644 index 281153a69a..0000000000 --- a/doc/doc2/compute_smd_rho.html +++ /dev/null @@ -1,54 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/rho command -

    -

    Syntax: -

    -
    compute ID group-ID smd/rho 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/rho = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/rho 
-
    -

    Description: -

    -

    Define a computation that calculates the per-particle mass density. -The mass density is the mass of a particle which is constant during -the course of a simulation, divided by its volume, which can change due to mechanical deformation. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle values will be in units of mass over volume. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    smd/vol -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_tlsph_defgrad.html b/doc/doc2/compute_smd_tlsph_defgrad.html deleted file mode 100644 index 56c52169db..0000000000 --- a/doc/doc2/compute_smd_tlsph_defgrad.html +++ /dev/null @@ -1,57 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/tlsph_defgrad command -

    -

    Syntax: -

    -
    compute ID group-ID smd/tlsph_defgrad 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/tlsph_defgrad = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/tlsph_defgrad 
-
    -

    Description: -

    -

    Define a computation that calculates the deformation gradient. -It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to use Smooth Mach Dynamics in -LAMMPS. -

    -

    Output info: -

    -

    This compute outputss a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle vector values will be given dimensionless. See units. -The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components -of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if LAMMPS was -built with that package. See the Making LAMMPS -section for more info. TThis compute can only be used for particles which interact via the -total Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/hourglass_error -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_tlsph_dt.html b/doc/doc2/compute_smd_tlsph_dt.html deleted file mode 100644 index bec2e7ca8a..0000000000 --- a/doc/doc2/compute_smd_tlsph_dt.html +++ /dev/null @@ -1,59 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/tlsph_dt command -

    -

    Syntax: -

    -
    compute ID group-ID smd/tlsph_dt 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/tlsph_dt = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/tlsph_dt 
-
    -

    Description: -

    -

    Define a computation that outputs the CFL-stable time increment per particle. -This time increment is essentially given by the speed of sound, divided by the SPH smoothing length. -Because both the speed of sound and the smoothing length typically change during the course of a simulation, -the stable time increment needs to be recomputed every time step. -This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the -stable time increment accessible for output purposes. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle values will be given in units of time. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/adjust_dt -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_tlsph_num_neighs.html b/doc/doc2/compute_smd_tlsph_num_neighs.html deleted file mode 100644 index 15a1ccdcae..0000000000 --- a/doc/doc2/compute_smd_tlsph_num_neighs.html +++ /dev/null @@ -1,55 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/tlsph_num_neighs command -

    -

    Syntax: -

    -
    compute ID group-ID smd/tlsph_num_neighs 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/tlsph_num_neighs = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/tlsph_num_neighs 
-
    -

    Description: -

    -

    Define a computation that calculates the number of particles -inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle values are dimensionless. See units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    This quantity will be computed only for particles which interact with the Total-Lagrangian pair style. -

    -

    Related commands: -

    -

    smd/ulsph_num_neighs -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_tlsph_shape.html b/doc/doc2/compute_smd_tlsph_shape.html deleted file mode 100644 index ff4557350e..0000000000 --- a/doc/doc2/compute_smd_tlsph_shape.html +++ /dev/null @@ -1,57 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/tlsph_shape command -

    -

    Syntax: -

    -
    compute ID group-ID smd/tlsph_shape 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/tlsph_shape = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/tlsph_shape 
-
    -

    Description: -

    -

    Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid. -It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of length. -These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle. -The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if LAMMPS was -built with that package. See the Making LAMMPS -section for more info. -

    -

    This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/contact_radius -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_tlsph_strain.html b/doc/doc2/compute_smd_tlsph_strain.html deleted file mode 100644 index d1a44dadc1..0000000000 --- a/doc/doc2/compute_smd_tlsph_strain.html +++ /dev/null @@ -1,58 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/tlsph_strain command -

    -

    Syntax: -

    -
    compute ID group-ID smd/tlsph_strain 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/tlsph_strain = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/tlsph_strain 
-
    -

    Description: -

    -

    Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See -How-to discussions, section 6.15 - for an overview of LAMMPS output options. -

    -

    The per-particle tensor values will be given dimensionless. See units. -

    -

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain tensor. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/tlsph_strain_rate, smd/tlsph_stress -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_tlsph_strain_rate.html b/doc/doc2/compute_smd_tlsph_strain_rate.html deleted file mode 100644 index 7705697208..0000000000 --- a/doc/doc2/compute_smd_tlsph_strain_rate.html +++ /dev/null @@ -1,57 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/tlsph_strain_rate command -

    -

    Syntax: -

    -
    compute ID group-ID smd/tlsph_strain_rate 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/tlsph_strain_rate = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/tlsph_strain_rate 
-
    -

    Description: -

    -

    Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The values will be given in units of one over time. -

    -

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/tlsph_strain, smd/tlsph_stress -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_tlsph_stress.html b/doc/doc2/compute_smd_tlsph_stress.html deleted file mode 100644 index 3f22be60cd..0000000000 --- a/doc/doc2/compute_smd_tlsph_stress.html +++ /dev/null @@ -1,58 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/tlsph_stress command -

    -

    Syntax: -

    -
    compute ID group-ID smd/tlsph_stress 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/tlsph_stress = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/tlsph_stress 
-
    -

    Description: -

    -

    Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The values will be given in units of pressure. -

    -

    The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components -of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., -the von Mises equivalent stress. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/tlsph_strain, smd/tlsph_strain_rate -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_triangle_mesh_vertices.html b/doc/doc2/compute_smd_triangle_mesh_vertices.html deleted file mode 100644 index a4fc72d701..0000000000 --- a/doc/doc2/compute_smd_triangle_mesh_vertices.html +++ /dev/null @@ -1,64 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - - - -
    - -

    compute smd/triangle_mesh_vertices -

    -

    Syntax: -

    -
    compute ID group-ID smd/triangle_mesh_vertices 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/triangle_mesh_vertices = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/triangle_mesh_vertices 
-
    -

    Description: -

    -

    Define a computation that returns the coordinates of the vertices -corresponding to the triangle-elements of a mesh created by the fix smd/wall_surface. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute returns a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute as -input. See How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding -to the first, second, and third vertex of each triangle. -

    -

    It is only meaningful to use this compute for a group of particles which is created via the -fix smd/wall_surface command. -

    -

    The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the -smd/wall_surace mesh for visualization purposes. -

    -

    The values will be given in units of distance. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    smd/move_tri_surf, smd/wall_surface -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_ulsph_num_neighs.html b/doc/doc2/compute_smd_ulsph_num_neighs.html deleted file mode 100644 index e3e1a43e85..0000000000 --- a/doc/doc2/compute_smd_ulsph_num_neighs.html +++ /dev/null @@ -1,53 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/ulsph_num_neighs command -

    -

    Syntax: -

    -
    compute ID group-ID smd/ulsph_num_neighs 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/ulsph_num_neighs = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/ulsph_num_neighs 
-
    -

    Description: -

    -

    Define a computation that returns the number of neighbor particles -inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute returns a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-particle values will be given dimentionless, see units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/tlsph_num_neighs -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_ulsph_strain.html b/doc/doc2/compute_smd_ulsph_strain.html deleted file mode 100644 index 8aca12a2a0..0000000000 --- a/doc/doc2/compute_smd_ulsph_strain.html +++ /dev/null @@ -1,56 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/ulsph_strain command -

    -

    Syntax: -

    -
    compute ID group-ID smd/ulsph_strain 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/ulsph_strain = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/ulsph_strain 
-
    -

    Description: -

    -

    Define a computation that outputs the logarithmic strain tensor. -for particles interacting via the updated Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle tensor, which can be accessed by -any command that uses per-particle values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor. -

    -

    The per-particle tensor values will be given dimensionless, see units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/tlsph_strain -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_ulsph_strain_rate.html b/doc/doc2/compute_smd_ulsph_strain_rate.html deleted file mode 100644 index 85015d69f5..0000000000 --- a/doc/doc2/compute_smd_ulsph_strain_rate.html +++ /dev/null @@ -1,56 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/ulsph_strain_rate command -

    -

    Syntax: -

    -
    compute ID group-ID smd/ulsph_strain_rate 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/ulsph_strain_rate = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/ulsph_strain_rate 
-
    -

    Description: -

    -

    Define a computation that outputs the rate of the logarithmic strain tensor -for particles interacting via the updated Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector of vectors (tensors), which -can be accessed by any command that uses per-particle values from a compute -as input. See Section_howto 15 for an overview of -LAMMPS output options. -

    -

    The values will be given in units of one over time. -

    -

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. -

    -

    Related commands: -

    -

    smd/utsph_strain_rate -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_ulsph_stress.html b/doc/doc2/compute_smd_ulsph_stress.html deleted file mode 100644 index 0af4d67087..0000000000 --- a/doc/doc2/compute_smd_ulsph_stress.html +++ /dev/null @@ -1,57 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/ulsph_stress command -

    -

    Syntax: -

    -
    compute ID group-ID smd/ulsph_stress 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/ulsph_stress = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/ulsph_stress 
-
    -

    Description: -

    -

    Define a computation that outputs the Cauchy stress tensor. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See Section_howto 15 -for an overview of LAMMPS output options. -

    -

    The values will be given in units of pressure. -

    -

    The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components -of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., -the von Mises equivalent stress. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. -

    -

    Related commands: -

    -
    smd/ulsph_strain, smd/ulsph_strain_rate
-smd/tlsph_stress 
-
    -

    Default: none -

    - diff --git a/doc/doc2/compute_smd_vol.html b/doc/doc2/compute_smd_vol.html deleted file mode 100644 index d0a1c70911..0000000000 --- a/doc/doc2/compute_smd_vol.html +++ /dev/null @@ -1,57 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute smd/vol command -

    -

    Syntax: -

    -
    compute ID group-ID smd/vol 
-
    -
    • ID, group-ID are documented in compute command -
    • smd/vol = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all smd/vol 
-
    -

    Description: -

    -

    Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the -group for which the fix is defined. -

    -

    See this PDF guide to using Smooth Mach Dynamics in -LAMMPS. -

    -

    Output info: -

    -

    This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options. -

    -

    The per-particle vector values will be given in units of volume. -

    -

    Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the -group for which the fix is defined. -

    -

    Restrictions: -

    -

    This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS - section for more info. -

    -

    Related commands: -

    -

    smd/rho -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_sna_atom.html b/doc/doc2/compute_sna_atom.html deleted file mode 100644 index 9e9b25d1d0..0000000000 --- a/doc/doc2/compute_sna_atom.html +++ /dev/null @@ -1,262 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute sna/atom command -

    -

    compute snad/atom command -

    -

    compute snav/atom command -

    -

    Syntax: -

    -
    compute ID group-ID sna/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-compute ID group-ID snad/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-compute ID group-ID snav/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • sna/atom = style name of this compute command - -
    • rcutfac = scale factor applied to all cutoff radii (positive real) - -
    • rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1) - -
    • twojmax = band limit for bispectrum components (non-negative integer) - -
    • R_1, R_2,... = list of cutoff radii, one for each type (distance units) - -
    • w_1, w_2,... = list of neighbor weights, one for each type - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = diagonal or rmin0 or switchflag - -
        diagonal value = 0 or 1 or 2 or 3
-     0 = all j1, j2, j <= twojmax, j2 <= j1
-     1 = subset satisfying j1 == j2
-     2 = subset satisfying j1 == j2 == j3
-     3 = subset satisfying j2 <= j1 <= j
-  rmin0 value = parameter in distance to angle conversion (distance units)
-  switchflag value = 0 or 1 
-     0 = do not use switching function
-     1 = use switching function 
-
      - -
    -

    Examples: -

    -
    compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 diagonal 3 rmin0 0.0
-compute db all sna/atom 1.4 0.95 6 2.0 1.0
-compute vb all sna/atom 1.4 0.95 6 2.0 1.0 
-
    -

    Description: -

    -

    Define a computation that calculates a set of bispectrum components -for each atom in a group. -

    -

    Bispectrum components of an atom are order parameters characterizing -the radial and angular distribution of neighbor atoms. The detailed -mathematical definition is given in the paper by Thompson et -al. (Thompson) -

    -

    The position of a neighbor atom i' relative to a central atom i is -a point within the 3D ball of radius R_ii' = rcutfac*(R_i + R_i') -

    -

    Bartok et al. (Bartok), proposed mapping this 3D ball -onto the 3-sphere, the surface of the unit ball in a four-dimensional -space. The radial distance r within R_ii' is mapped on to a third -polar angle theta0 defined by, -

    -
    -
    -

    In this way, all possible neighbor positions are mapped on to a subset -of the 3-sphere. Points south of the latitude theta0max=rfac0*Pi -are excluded. -

    -

    The natural basis for functions on the 3-sphere is formed by the 4D -hyperspherical harmonics U^j_m,m'(theta, phi, theta0). These -functions are better known as D^j_m,m', the elements of the Wigner -D-matrices (Meremianin, -Varshalovich). -

    -

    The density of neighbors on the 3-sphere can be written as a sum of -Dirac-delta functions, one for each neighbor, weighted by species and -radial distance. Expanding this density function as a generalized -Fourier series in the basis functions, we can write each Fourier -coefficient as -

    -
    -
    -

    The w_i' neighbor weights are dimensionless numbers that are chosen -to distinguish atoms of different types, while the central atom is -arbitrarily assigned a unit weight. The function fc(r) ensures that -the contribution of each neighbor atom goes smoothly to zero at -R_ii': -

    -
    -
    -

    The expansion coefficients u^j_m,m' are complex-valued and they are -not directly useful as descriptors, because they are not invariant -under rotation of the polar coordinate frame. However, the following -scalar triple products of expansion coefficients can be shown to be -real-valued and invariant under rotation (Bartok). -

    -
    -
    -

    The constants H^jmm'_j1m1m1'_j2m2m2' are coupling coefficients, -analogous to Clebsch-Gordan coefficients for rotations on the -2-sphere. These invariants are the components of the bispectrum and -these are the quantities calculated by the compute sna/atom. They -characterize the strength of density correlations at three points on -the 3-sphere. The j2=0 subset form the power spectrum, which -characterizes the correlations of two points. The lowest-order -components describe the coarsest features of the density function, -while higher-order components reflect finer detail. Note that the -central atom is included in the expansion, so three point-correlations -can be either due to three neighbors, or two neighbors and the central -atom. -

    -

    Compute snad/atom calculates the derivative of the bispectrum components -summed separately for each atom type: -

    -
    -
    -

    The sum is over all atoms i' of atom type I. For each atom i, -this compute evaluates the above expression for each direction, each -atom type, and each bispectrum component. See section below on output -for a detailed explanation. -

    -

    Compute snav/atom calculates the virial contribution due to the -derivatives: -

    -
    -
    -

    Again, the sum is over all atoms i' of atom type I. For each atom -i, this compute evaluates the above expression for each of the six -virial components, each atom type, and each bispectrum component. See -section below on output for a detailed explanation. -

    -

    The value of all bispectrum components will be zero for atoms not in -the group. Neighbor atoms not in the group do not contribute to the -bispectrum of atoms in the group. -

    -

    The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. -

    -

    The argument rcutfac is a scale factor that controls the ratio of -atomic radius to radial cutoff distance. -

    -

    The argument rfac0 and the optional keyword rmin0 define the -linear mapping from radial distance to polar angle theta0 on the -3-sphere. -

    -

    The argument twojmax and the keyword diagonal define which -bispectrum components are generated. See section below on output for a -detailed explanation of the number of bispectrum components and the -ordered in which they are listed -

    -

    The keyword switchflag can be used to turn off the switching -function. -

    -

    IMPORTANT NOTE: If you have a bonded system, then the settings of -special_bonds command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the special_bonds -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the calculation. One way to get -around this, is to write a dump file, and use the rerun -command to compute the bispectrum components for snapshots in the dump -file. The rerun script can use a special_bonds -command that includes all pairs in the neighbor list. -

    -

    ;line -

    -

    Output info: -

    -

    Compute sna/atom calculates a per-atom array, each column -corresponding to a particular bispectrum component. The total number -of columns and the identities of the bispectrum component contained in -each column depend on the values of twojmax and diagonal, as -described by the following piece of python code: -

    -
    for j1 in range(0,twojmax+1):
-    if(diagonal==2): 
-        print j1/2,j1/2,j1/2
-    elif(diagonal==1):
-        for j in range(0,min(twojmax,2*j1)+1,2): 
-            print j1/2,j1/2,j/2
-    elif(diagonal==0):
-        for j2 in range(0,j1+1):
-            for j in range(j1-j2,min(twojmax,j1+j2)+1,2): 
-                print j1/2,j2/2,j/2
-    elif(diagonal==3):
-        for j2 in range(0,j1+1):
-            for j in range(j1-j2,min(twojmax,j1+j2)+1,2): 
-                if (j>=j1): print j1/2,j2/2,j/2 
-
    -

    Compute snad/atom evaluates a per-atom array. The columns are -arranged into ntypes blocks, listed in order of atom type I. Each -block contains three sub-blocks corresponding to the x, y, and z -components of the atom position. Each of these sub-blocks contains -one column for each bispectrum component, the same as for compute -sna/atom -

    -

    Compute snav/atom evaluates a per-atom array. The columns are -arranged into ntypes blocks, listed in order of atom type I. Each -block contains six sub-blocks corresponding to the xx, yy, zz, -yz, xz, and xy components of the virial tensor in Voigt -notation. Each of these sub-blocks contains one column for each -bispectrum component, the same as for compute sna/atom -

    -

    These values can be accessed by any command that uses per-atom values -from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    Restrictions: -

    -

    These computes are part of the SNAP package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_style snap -

    -

    Default: -

    -

    The optional keyword defaults are diagonal = 0, rmin0 = 0, -switchflag = 1. -

    -
    - - - -

    (Thompson) Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint -available at arXiv:1409.3880 -

    - - -

    (Bartok) Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). -

    - - -

    (Meremianin) Meremianin, J. Phys. A, 39, 3099 (2006). -

    - - -

    (Varshalovich) Varshalovich, Moskalev, Khersonskii, Quantum Theory -of Angular Momentum, World Scientific, Singapore (1987). -

    - diff --git a/doc/doc2/compute_stress_atom.html b/doc/doc2/compute_stress_atom.html deleted file mode 100644 index 52089c9aef..0000000000 --- a/doc/doc2/compute_stress_atom.html +++ /dev/null @@ -1,172 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute stress/atom command -

    -

    Syntax: -

    -
    compute ID group-ID stress/atom temp-ID keyword ... 
-
    -
    • ID, group-ID are documented in compute command -
    • stress/atom = style name of this compute command -
    • temp-ID = ID of compute that calculates temperature, can be NULL if not needed -
    • zero or more keywords may be appended -
    • keyword = ke or pair or bond or angle or dihedral or improper or kspace or fix or virial -
    -

    Examples: -

    -
    compute 1 mobile stress/atom NULL
-compute 1 mobile stress/atom myRamp
-compute 1 all stress/atom NULL pair bond 
-
    -

    Description: -

    -

    Define a computation that computes the symmetric per-atom stress -tensor for each atom in a group. The tensor for each atom has 6 -components and is stored as a 6-element vector in the following order: -xx, yy, zz, xy, xz, yz. See the compute -pressure command if you want the stress tensor -(pressure) of the entire system. -

    -

    The stress tensor for atom I is given by the following formula, -where a and b take on values x,y,z to generate the 6 components of -the symmetric tensor: -

    -
    -
    -

    The first term is a kinetic energy contribution for atom I. See -details below on how the specified temp-ID can affect the velocities -used in this calculation. The second term is a pairwise energy -contribution where n loops over the Np neighbors of atom I, r1 -and r2 are the positions of the 2 atoms in the pairwise interaction, -and F1 and F2 are the forces on the 2 atoms resulting from the -pairwise interaction. The third term is a bond contribution of -similar form for the Nb bonds which atom I is part of. There are -similar terms for the Na angle, Nd dihedral, and Ni improper -interactions atom I is part of. There is also a term for the KSpace -contribution from long-range Coulombic interactions, if defined. -Finally, there is a term for the Nf fixes that apply -internal constraint forces to atom I. Currently, only the fix -shake and fix rigid commands -contribute to this term. -

    -

    As the coefficients in the formula imply, a virial contribution -produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3 -atoms in a Tersoff 3-body interaction) is assigned in equal portions -to each atom in the set. E.g. 1/4 of the dihedral virial to each of -the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied -to atoms in a a water molecule via the fix shake -command. -

    -

    If no extra keywords are listed, all of the terms in this formula are -included in the per-atom stress tensor. If any extra keywords are -listed, only those terms are summed to compute the tensor. The -virial keyword means include all terms except the kinetic energy -ke. -

    -

    Note that the stress for each atom is due to its interaction with all -other atoms in the simulation, not just with other atoms in the group. -

    -

    Details of how LAMMPS computes the virial for individual atoms for -either pairwise or manybody potentials, and including the effects of -periodic boundary conditions is discussed in (Thompson). -The basic idea for manybody potentials is to treat each component of -the force computation between a small cluster of atoms in the same -manner as in the formula above for bond, angle, dihedral, etc -interactions. Namely the quantity R dot F is summed over the atoms in -the interaction, with the R vectors unwrapped by periodic boundaries -so that the cluster of atoms is close together. The total -contribution for the cluster interaction is divided evenly among those -atoms. -

    -

    The dihedral_style charmm style calculates -pairwise interactions between 1-4 atoms. The virial contribution of -these terms is included in the pair virial, not the dihedral virial. -

    -

    The KSpace contribution is calculated using the method in -(Heyes) for the Ewald method and by the methodology described -in (Sirk) for PPPM. The choice of KSpace solver is specified -by the kspace_style pppm command. Note that for -PPPM, the calcluation requires 6 extra FFTs each timestep that -per-atom stress is calculated. Thus it can significantly increase the -cost of the PPPM calculation if it is needed on a large fraction of -the simulation timesteps. -

    -

    The temp-ID argument can be used to affect the per-atom velocities -used in the kinetic energy contribution to the total stress. If the -kinetic energy is not included in the stress, than the temperature -compute is not used and can be specified as NULL. If the kinetic -energy is included and you wish to use atom velocities as-is, then -temp-ID can also be specified as NULL. If desired, the specified -temperature compute can be one that subtracts off a bias to leave each -atom with only a thermal velocity to use in the formula above, e.g. by -subtracting a background streaming velocity. See the doc pages for -individual compute commands to determine which ones -include a bias. -

    -
    - -

    Note that as defined in the formula, per-atom stress is the negative -of the per-atom pressure tensor. It is also really a stress*volume -formulation, meaning the computed quantity is in units of -pressure*volume. It would need to be divided by a per-atom volume to -have units of stress (pressure), but an individual atom's volume is -not well defined or easy to compute in a deformed solid or a liquid. -See the compute voronoi/atom command for -one possible way to estimate a per-atom volume. -

    -

    Thus, if the diagonal components of the per-atom stress tensor are -summed for all atoms in the system and the sum is divided by dV, where -d = dimension and V is the volume of the system, the result should be --P, where P is the total pressure of the system. -

    -

    These lines in an input script for a 3d system should yield that -result. I.e. the last 2 columns of thermo output will be the same: -

    -
    compute		peratom all stress/atom NULL
-compute		p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
-variable	press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
-thermo_style	custom step temp etotal press v_press 
-
    -

    Output info: -

    -

    This compute calculates a per-atom array with 6 columns, which can be -accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The per-atom array values will be in pressure*volume -units as discussed above. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute pe, compute pressure -

    -

    Default: none -

    -
    - - - -

    (Heyes) Heyes, Phys Rev B 49, 755 (1994), -

    - - -

    (Sirk) Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013). -

    - - -

    (Thompson) Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). -

    - diff --git a/doc/doc2/compute_tally.html b/doc/doc2/compute_tally.html deleted file mode 100644 index ec462629dd..0000000000 --- a/doc/doc2/compute_tally.html +++ /dev/null @@ -1,92 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute force/tally command -

    -

    compute heat/flux/tally command -

    -

    compute pe/tally command -

    -

    compute stress/tally command -

    -

    Syntax: -

    -
    compute ID group-ID style group2-ID 
-
    -
    • ID, group-ID are documented in compute command -
    • style = force/tally or pe/tally or stress/tally -
    • group2-ID = group ID of second (or same) group -
    -

    Examples: -

    -
    compute 1 lower force/tally upper
-compute 1 left pe/tally right
-compute 1 lower stress/tally lower 
-
    -

    Description: -

    -

    Define a computation that calculates properties between two groups of -atoms by accumulating them from pairwise non-bonded computations. The -two groups can be the same. This is similar to compute -group/group only that the data is -accumulated directly during the non-bonded force computation. The -computes force/tally, pe/tally, stress/tally, and -heat/flux/tally are primarily provided as example how to program -additional, more sophisticated computes using the tally mechanism. -

    -
    - -

    The pairwise contributions are computing via a callback that the -compute registers with the non-bonded pairwise force computation. -This limits the use to systems that have no bonds, no Kspace, and no -manybody interactions. On the other hand, the computation does not -have to compute forces or energies a second time and thus can be much -more efficient. The callback mechanism allows to write more complex -pairwise property computations. -

    -
    - -

    Output info: -

    -

    Compute pe/tally calculates a global scalar (the energy) and a per -atom scalar (the contributions of the single atom to the global -scalar). Compute force/tally calculates a global scalar (the force -magnitude) and a per atom 3-element vector (force contribution from -each atom). Compute stress/tally calculates a global scalar -(average of the diagonal elements of the stress tensor) and a per atom -vector (the 6 elements of stress tensor contributions from the -individual atom). -

    -

    Both the scalar and vector values calculated by this compute are -"extensive". -

    -

    Restrictions: -

    -

    This compute is part of the USER-TALLY package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Not all pair styles can be evaluated in a pairwise mode as required by -this compute. For example, 3-body and other many-body potentials, -such as Tersoff and -Stillinger-Weber cannot be used. EAM -potentials only include the pair potential portion of the EAM -interaction when used by this compute, not the embedding term. Also -bonded or Kspace interactions do not contribute to this compute. -

    -

    Related commands: -

    -

    compute group/group_compute_group_group.html, compute -heat/flux_compute_heat_flux.html -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp.html b/doc/doc2/compute_temp.html deleted file mode 100644 index 13905f6532..0000000000 --- a/doc/doc2/compute_temp.html +++ /dev/null @@ -1,121 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp command -

    -

    compute temp/cuda command -

    -

    compute temp/kk command -

    -

    Syntax: -

    -
    compute ID group-ID temp 
-
    -
    • ID, group-ID are documented in compute command -
    • temp = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all temp
-compute myTemp mobile temp 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms. A compute of this style can be used by any command that -computes a temperature, e.g. thermo_modify, fix -temp/rescale, fix npt, etc. -

    -

    The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    A compute of this style with the ID of "thermo_temp" is created when -LAMMPS starts up, as if this command were in the input script: -

    -
    compute thermo_temp all temp 
-
    -

    See the "thermo_style" command for more details. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp/partial, compute -temp/region, compute -pressure -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_asphere.html b/doc/doc2/compute_temp_asphere.html deleted file mode 100644 index 2c6241da99..0000000000 --- a/doc/doc2/compute_temp_asphere.html +++ /dev/null @@ -1,163 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/asphere command -

    -

    Syntax: -

    -
    compute ID group-ID temp/asphere keyword value ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • temp/asphere = style name of this compute command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = bias or dof - -
        bias value = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias
-  dof value = all or rotate
-    all = compute temperature of translational and rotational degrees of freedom
-    rotate = compute temperature of just rotational degrees of freedom 
-
      - -
    -

    Examples: -

    -
    compute 1 all temp/asphere
-compute myTemp mobile temp/asphere bias tempCOM
-compute myTemp mobile temp/asphere dof rotate 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -aspherical particles, including a contribution from both their -translational and rotational kinetic energy. This differs from the -usual compute temp command, which assumes point -particles with only translational kinetic energy. -

    -

    Only finite-size particles (aspherical or spherical) can be included -in the group. For 3d finite-size particles, each has 6 degrees of -freedom (3 translational, 3 rotational). For 2d finite-size -particles, each has 3 degrees of freedom (2 translational, 1 -rotational). -

    -

    IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that -all finite-size aspherical or spherical particles in your model will -freely rotate, sampling all their rotational dof. It is possible to -use a combination of interaction potentials and fixes that induce no -torque or otherwise constrain some of all of your particles so that -this is not the case. Then there are less dof and you should use the -compute_modify extra command to adjust the dof -accordingly. -

    -

    For example, an aspherical particle with all three of its shape -parameters the same is a sphere. If it does not rotate, then it -should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A -uniaxial aspherical particle has two of its three shape parameters the -same. If it does not rotate around the axis perpendicular to its -circular cross section, then it should have 5 dof instead of 6 in 3d. -The latter is the case for uniaxial ellipsoids in a GayBerne -model since there is no induced torque around the -optical axis. It will also be the case for biaxial ellipsoids when -exactly two of the semiaxes have the same length and the corresponding -relative well depths are equal. -

    -

    The translational kinetic energy is computed the same as is described -by the compute temp command. The rotational -kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor -for the aspherical particle and w is its angular velocity, which is -computed from its angular momentum. -

    -

    IMPORTANT NOTE: For 2d models, particles are treated -as ellipsoids, not ellipses, meaning their moments of inertia will be -the same as in 3d. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute. The formula for the components of the -tensor is the same as the above formula, except that v^2 and w^2 are -replaced by vx*vy and wx*wy for the xy component, and the appropriate -elements of the inertia tensor are used. The 6 components of the -vector are ordered xx, yy, zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    This compute subtracts out translational degrees-of-freedom due to -fixes that constrain molecular motion, such as fix -shake and fix rigid. This means the -temperature of groups of atoms that include these constraints will be -computed correctly. If needed, the subtracted degrees-of-freedom can -be altered using the extra option of the -compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -
    - -

    The keyword/value option pairs are used in the following ways. -

    -

    For the bias keyword, bias-ID refers to the ID of a temperature -compute that removes a "bias" velocity from each atom. This allows -compute temp/sphere to compute its thermal temperature after the -translational kinetic energy components have been altered in a -prescribed way, e.g. to remove a flow velocity profile. Thermostats -that use this compute will work with this bias term. See the doc -pages for individual computes that calculate a temperature and the doc -pages for fixes that perform thermostatting for more details. -

    -

    For the dof keyword, a setting of all calculates a temperature -that includes both translational and rotational degrees of freedom. A -setting of rotate calculates a temperature that includes only -rotational degrees of freedom. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This compute requires that atoms store angular momementum and a -quaternion as defined by the atom_style ellipsoid -command. -

    -

    All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. -

    -

    Related commands: -

    -

    compute temp -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_chunk.html b/doc/doc2/compute_temp_chunk.html deleted file mode 100644 index 05947ba736..0000000000 --- a/doc/doc2/compute_temp_chunk.html +++ /dev/null @@ -1,251 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • temp/chunk = style name of this compute command - -
    • chunkID = ID of compute chunk/atom command - -
    • zero or more values can be listed as value1,value2,etc - -
    • value = temp or kecom or internal - -
        temp = temperature of each chunk
-  kecom = kinetic energy of each chunk based on velocity of center of mass
-  internal = internal kinetic energy of each chunk 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = com or bias or adof or cdof - -
        com value = yes or no
-    yes = subtract center-of-mass velocity from each chunk before calculating temperature
-    no = do not subtract center-of-mass velocity
-  bias value = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias
-  adof value = dof_per_atom
-    dof_per_atom = define this many degrees-of-freedom per atom
-  cdof value = dof_per_chunk
-    dof_per_chunk = define this many degrees-of-freedom per chunk 
-
      - -
    -

    Examples: -

    -
    compute 1 fluid temp/chunk molchunk
-compute 1 fluid temp/chunk molchunk temp internal
-compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms that are also in chunks, after optionally subtracting out the -center-of-mass velocity of each chunk. By specifying optional values, -it can also calulate the per-chunk temperature or energies of the -multiple chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    The temperature is calculated by the formula KE = DOF/2 k T, where KE = -total kinetic energy of all atoms assigned to chunks (sum of 1/2 m -v^2), DOF = the total number of degrees of freedom for those atoms, k -= Boltzmann constant, and T = temperature. -

    -

    The DOF is calculated as N*adof + Nchunk*cdof, where N = number of -atoms contributing to the KE, adof = degrees of freedom per atom, and -cdof = degrees of freedom per chunk. By default adof = 2 or 3 = -dimensionality of system, as set via the dimension -command, and cdof = 0.0. This gives the usual formula for -temperature. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    Note that the number of atoms contributing to the temperature is -calculated each time the temperature is evaluated since it is assumed -the atoms may be dynamically assigned to chunks. Thus there is no -need to use the dynamic option of the -compute_modify command for this compute style. -

    -

    If any optional values are specified, then per-chunk quantities are -also calculated and stored in a global array, as described below. -

    -

    The temp value calculates the temperature for each chunk by the -formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk -of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of -freedom for all atoms in the chunk, k = Boltzmann constant, and T = -temperature. -

    -

    The DOF in this case is calculated as N*adof + cdof, where N = number -of atoms in the chunk, adof = degrees of freedom per atom, and cdof = -degrees of freedom per chunk. By default adof = 2 or 3 = -dimensionality of system, as set via the dimension -command, and cdof = 0.0. This gives the usual formula for -temperature. -

    -

    The kecom value calculates the kinetic energy of each chunk as if -all its atoms were moving with the velocity of the center-of-mass of -the chunk. -

    -

    The internal value calculates the internal kinetic energy of each -chunk. The interal KE is summed over the atoms in the chunk using an -internal "thermal" velocity for each atom, which is its velocity minus -the center-of-mass velocity of the chunk. -

    -
    - -

    Note that currently the global and per-chunk temperatures calculated -by this compute only include translational degrees of freedom for each -atom. No rotational degrees of freedom are included for finite-size -particles. Also no degrees of freedom are subtracted for any velocity -bias or constraints that are applied, such as compute -temp/partial, or fix shake -or fix rigid. This is because those degrees of -freedom (e.g. a constrained bond) could apply to sets of atoms that -are both included and excluded from a specific chunk, and hence the -concept is somewhat ill-defined. In some cases, you can use the -adof and cdof keywords to adjust the calculated degress of freedom -appropriately, as explained below. -

    -

    Note that the per-chunk temperature calulated by this compute and the -fix ave/chunk temp command can be different. -This compute calculates the temperature for each chunk for a single -snapshot. Fix ave/chunk can do that but can also time average those -values over many snapshots, or it can compute a temperature as if the -atoms in the chunk on different timesteps were collected together as -one set of atoms to calculate their temperature. This compute allows -the center-of-mass velocity of each chunk to be subtracted before -calculating the temperature; fix ave/chunk does not. -

    -

    IMPORTANT NOTE: Only atoms in the specified group contribute to the -calculations performed by this compute. The compute -chunk/atom command defines its own group; -atoms will have a chunk ID = 0 if they are not in that group, -signifying they are not assigned to a chunk, and will thus also not -contribute to this calculation. You can specify the "all" group for -this command if you simply want to include atoms with non-zero chunk -IDs. -

    -

    The simplest way to output the per-chunk results of the compute -temp/chunk calculation to a file is to use the fix -ave/time command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all temp/chunk cc1 temp
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -
    - -

    The keyword/value option pairs are used in the following ways. -

    -

    The com keyword can be used with a value of yes to subtract the -velocity of the center-of-mass for each chunk from the velocity of the -atoms in that chunk, before calculating either the global or per-chunk -temperature. This can be useful if the atoms are streaming or -otherwise moving collectively, and you wish to calculate only the -thermal temperature. -

    -

    For the bias keyword, bias-ID refers to the ID of a temperature -compute that removes a "bias" velocity from each atom. This also -allows calculation of the global or per-chunk temperature using only -the thermal temperature of atoms in each chunk after the translational -kinetic energy components have been altered in a prescribed way, -e.g. to remove a velocity profile. It also applies to the calculation -of the other per-chunk values, such as kecom or internal, which -involve the center-of-mass velocity of each chunk, which is calculated -after the velocity bias is removed from each atom. Note that the -temperature compute will apply its bias globally to the entire system, -not on a per-chunk basis. -

    -

    The adof and cdof keywords define the values used in the degree of -freedom (DOF) formulas used for the global or per-chunk temperature, -as described above. They can be used to calculate a more appropriate -temperature for some kinds of chunks. Here are 3 examples: -

    -

    If spatially binned chunks contain some number of water molecules and -fix shake is used to make each molecule rigid, then -you could calculate a temperature with 6 degrees of freedom (DOF) (3 -translational, 3 rotational) per molecule by setting adof to 2.0. -

    -

    If compute temp/partial is used with the -bias keyword to only allow the x component of velocity to contribute -to the temperature, then adof = 1.0 would be appropriate. -

    -

    If each chunk consists of a large molecule, with some number of its -bonds constrained by fix shake or the entire molecule -by fix rigid/small, adof = 0.0 and cdof could be -set to the remaining degrees of freedom for the entire molecule -(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid -molecule. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    This compute also optionally calculates a global array, if one or more -of the optional values are specified. The number of rows in the array -= the number of chunks Nchunk as calculated by the specified -compute chunk/atom command. The number of -columns is the number of specifed values (1 or more). These values -can be accessed by any command that uses global array values from a -compute as input. Again, see Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". The array values are "intensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. The array values -will be in temperature units for the temp value, and in -energy units for the kecom and internal values. -

    -

    Restrictions: -

    -

    The com and bias keywords cannot be used together. -

    -

    Related commands: -

    -

    compute temp, fix ave/chunk -temp -

    -

    Default: -

    -

    The option defaults are com no, no bias, adof = dimensionality of the -system (2 or 3), and cdof = 0.0. -

    - diff --git a/doc/doc2/compute_temp_com.html b/doc/doc2/compute_temp_com.html deleted file mode 100644 index 5635c606d3..0000000000 --- a/doc/doc2/compute_temp_com.html +++ /dev/null @@ -1,98 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/com command -

    -

    Syntax: -

    -
    compute ID group-ID temp/com 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/com = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all temp/com
-compute myTemp mobile temp/com 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms, after subtracting out the center-of-mass velocity of the group. -This is useful if the group is expected to have a non-zero net -velocity for some reason. A compute of this style can be used by any -command that computes a temperature, -e.g. thermo_modify, fix -temp/rescale, fix npt, etc. -

    -

    After the center-of-mass velocity has been subtracted from each atom, -the temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    The removal of the center-of-mass velocity by this fix is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. If this compute is used with a fix command -that performs thermostatting then this bias will be subtracted from -each atom, thermostatting of the remaining thermal velocity will be -performed, and the bias will be added back in. Thermostatting fixes -that work in this way include fix nvt, fix -temp/rescale, fix -temp/berendsen, and fix -langevin. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_cs.html b/doc/doc2/compute_temp_cs.html deleted file mode 100644 index cf8fdbedc6..0000000000 --- a/doc/doc2/compute_temp_cs.html +++ /dev/null @@ -1,125 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/cs command -

    -

    Syntax: -

    -
    compute ID group-ID temp/cs group1 group2 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/cs = style name of this compute command -
    • group1 = group-ID of either cores or shells -
    • group2 = group-ID of either shells or cores -
    -

    Examples: -

    -
    compute oxygen_c-s all temp/cs O_core O_shell
-compute core_shells all temp/cs cores shells 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a system based -on the center-of-mass velocity of atom pairs that are bonded to each -other. This compute is designed to be used with the adiabatic -core/shell model of (Mitchell and Finchham). See -Section_howto 25 of the manual for an -overview of the model as implemented in LAMMPS. Specifically, this -compute enables correct temperature calculation and thermostatting of -core/shell pairs where it is desirable for the internal degrees of -freedom of the core/shell pairs to not be influenced by a thermostat. -A compute of this style can be used by any command that computes a -temperature via fix_modify e.g. fix -temp/rescale, fix npt, etc. -

    -

    Note that this compute does not require all ions to be polarized, -hence defined as core/shell pairs. One can mix core/shell pairs and -ions without a satellite particle if desired. The compute will -consider the non-polarized ions according to the physical system. -

    -

    For this compute, core and shell particles are specified by two -respective group IDs, which can be defined using the -group command. The number of atoms in the two groups -must be the same and there should be one bond defined between a pair -of atoms in the two groups. Non-polarized ions which might also be -included in the treated system should not be included into either of -these groups, they are taken into account by the group-ID (2nd -argument) of the compute. -

    -

    The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. Note that -the velocity of each core or shell atom used in the KE calculation is -the velocity of the center-of-mass (COM) of the core/shell pair the -atom is part of. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. In contrast to the temperature, the velocity of -each core or shell atom is taken individually. -

    -

    The change this fix makes to core/shell atom velocities is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. This "bias" is the velocity of the atom -relative to the COM velocity of the core/shell pair. If this compute -is used with a fix command that performs thermostatting then this bias -will be subtracted from each atom, thermostatting of the remaining COM -velocity will be performed, and the bias will be added back in. This -means the thermostating will effectively be performed on the -core/shell pairs, instead of on the individual core and shell atoms. -Thermostatting fixes that work in this way include fix -nvt, fix temp/rescale, fix -temp/berendsen, and fix -langevin. -

    -

    The internal energy of core/shell pairs can be calculated by the -compute temp/chunk command, if chunks are -defined as core/shell pairs. See Section_howto -25 for more discussion on how to do this. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: -

    -

    The number of core/shell pairs contributing to the temperature is -assumed to be constant for the duration of the run. No fixes should -be used which generate new molecules or atoms during a simulation. -

    -

    Related commands: -

    -

    compute temp, compute -temp/chunk -

    -

    Default: none -

    -
    - - - -

    (Mitchell and Finchham) Mitchell, Finchham, J Phys Condensed Matter, -5, 1031-1038 (1993). -

    - diff --git a/doc/doc2/compute_temp_deform.html b/doc/doc2/compute_temp_deform.html deleted file mode 100644 index 1a2af61281..0000000000 --- a/doc/doc2/compute_temp_deform.html +++ /dev/null @@ -1,139 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/deform command -

    -

    Syntax: -

    -
    compute ID group-ID temp/deform 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/deform = style name of this compute command -
    -

    Examples: -

    -
    compute myTemp all temp/deform 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms, after subtracting out a streaming velocity induced by the -simulation box changing size and/or shape, for example in a -non-equilibrium MD (NEMD) simulation. The size/shape change is -induced by use of the fix deform command. A compute -of this style is created by the fix nvt/sllod -command to compute the thermal temperature of atoms for thermostatting -purposes. A compute of this style can also be used by any command -that computes a temperature, e.g. thermo_modify, -fix temp/rescale, fix npt, etc. -

    -

    The deformation fix changes the box size and/or shape over time, so -each atom in the simulation box can be thought of as having a -"streaming" velocity. For example, if the box is being sheared in x, -relative to y, then atoms at the bottom of the box (low y) have a -small x velocity, while atoms at the top of the box (hi y) have a -large x velocity. This position-dependent streaming velocity is -subtracted from each atom's actual velocity to yield a thermal -velocity which is used to compute the temperature. -

    -

    IMPORTANT NOTE: Fix deform has an option for -remapping either atom coordinates or velocities to the changing -simulation box. When using this compute in conjunction with a -deforming box, fix deform should NOT remap atom positions, but rather -should let atoms respond to the changing box by adjusting their own -velocities (or let fix deform remap the atom -velocities, see it's remap option). If fix deform does remap atom -positions, then they appear to move with the box but their velocity is -not changed, and thus they do NOT have the streaming velocity assumed -by this compute. LAMMPS will warn you if fix deform is defined and -its remap setting is not consistent with this compute. -

    -

    After the streaming velocity has been subtracted from each atom, the -temperature is calculated by the formula KE = dim/2 N k T, where KE = -total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 -or 3 = dimensionality of the simulation, N = number of atoms in the -group, k = Boltzmann constant, and T = temperature. Note that v in -the kinetic energy formula is the atom's thermal velocity. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    The removal of the box deformation velocity component by this fix is -essentially computing the temperature after a "bias" has been removed -from the velocity of the atoms. If this compute is used with a fix -command that performs thermostatting then this bias will be subtracted -from each atom, thermostatting of the remaining thermal velocity will -be performed, and the bias will be added back in. Thermostatting -fixes that work in this way include fix nvt, fix -temp/rescale, fix -temp/berendsen, and fix -langevin. -

    -

    IMPORTANT NOTE: The temperature calculated by this compute is only -accurate if the atoms are indeed moving with a stream velocity profile -that matches the box deformation. If not, then the compute will -subtract off an incorrect stream velocity, yielding a bogus thermal -temperature. You should NOT assume that your atoms are streaming at -the same rate the box is deforming. Rather, you should monitor their -velocity profile, e.g. via the fix ave/spatial -command. And you can compare the results of this compute to compute -temp/profile, which actually calculates the -stream profile before subtracting it. If the two computes do not give -roughly the same temperature, then your atoms are not streaming -consistent with the box deformation. See the fix -deform command for more details on ways to get atoms -to stream consistently with the box deformation. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp/ramp, compute -temp/profile, fix deform, -fix nvt/sllod -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_deform_eff.html b/doc/doc2/compute_temp_deform_eff.html deleted file mode 100644 index 6331c8e915..0000000000 --- a/doc/doc2/compute_temp_deform_eff.html +++ /dev/null @@ -1,78 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/deform/eff command -

    -

    Syntax: -

    -
    compute ID group-ID temp/deform/eff 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/deform/eff = style name of this compute command -
    -

    Examples: -

    -
    compute myTemp all temp/deform/eff 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -nuclei and electrons in the electron force field -model, after subtracting out a streaming velocity induced by the -simulation box changing size and/or shape, for example in a -non-equilibrium MD (NEMD) simulation. The size/shape change is -induced by use of the fix deform/eff command. A -compute of this style is created by the fix -nvt/sllod/eff command to compute the thermal -temperature of atoms for thermostatting purposes. A compute of this -style can also be used by any command that computes a temperature, -e.g. thermo_modify, fix npt/eff, -etc. -

    -

    The calculation performed by this compute is exactly like that -described by the compute temp/deform -command, except that the formula for the temperature includes the -radial electron velocity contributions, as discussed by the compute -temp/eff command. Note that only the -translational degrees of freedom for each nuclei or electron are -affected by the streaming velocity adjustment. The radial velocity -component of the electrons is not affected. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute temp/ramp, fix -deform/eff, fix -nvt/sllod/eff -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_drude.html b/doc/doc2/compute_temp_drude.html deleted file mode 100644 index 96d3aac384..0000000000 --- a/doc/doc2/compute_temp_drude.html +++ /dev/null @@ -1,87 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/drude command -

    -

    Syntax: -

    -
    compute ID group-ID temp/drude 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/drude = style name of this compute command -
    -

    Examples: -

    -
    compute TDRUDE all temp/drude 
-
    -

    Description: -

    -

    Define a computation that calculates the temperatures of core-Drude -pairs. This compute is designed to be used with the thermalized Drude -oscillator model. This compute is designed to be used with the -thermalized Drude oscillator model. Polarizable -models in LAMMPS are described in this -Section. -

    -

    Drude oscillators consist of a core particle and a Drude particle -connected by a harmonic bond, and the relative motion of these Drude -oscillators is usually maintained cold by a specific thermostat that -acts on the relative motion of the core-Drude particle -pairs. Therefore, because LAMMPS considers Drude particles as normal -atoms in its default temperature compute (compute -temp command), the reduced temperature of the -core-Drude particle pairs is not calculated correctly. -

    -

    By contrast, this compute calculates the temperature of the cores -using center-of-mass velocities of the core-Drude pairs, and the -reduced temperature of the Drude particles using the relative -velocities of the Drude particles with respect to their cores. -Non-polarizable atoms are considered as cores. Their velocities -contribute to the temperature of the cores. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6, which can be accessed by indices 1-6, whose components -are -

    -
    1. temperature of the centers of mass (temperature units) -
    2. temperature of the dipoles (temperature units) -
    3. number of degrees of freedom of the centers of mass -
    4. number of degrees of freedom of the dipoles -
    5. kinetic energy of the centers of mass (energy units) -
    6. kinetic energy of the dipoles (energy units) -
    -

    These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    Both the scalar value and the first two values of the vector -calculated by this compute are "intensive". The other 4 vector values -are "extensive". -

    -

    Restrictions: -

    -

    The number of degrees of freedom contributing to the temperature is -assumed to be constant for the duration of the run unless the -fix_modify command sets the option dynamic yes. -

    -

    Related commands: -

    -

    fix drude, fix -langevin_drude, fix -drude/transform, pair_style -thole, compute temp -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_eff.html b/doc/doc2/compute_temp_eff.html deleted file mode 100644 index 3cc20e9db7..0000000000 --- a/doc/doc2/compute_temp_eff.html +++ /dev/null @@ -1,100 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/eff command -

    -

    Syntax: -

    -
    compute ID group-ID temp/eff 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/eff = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all temp/eff
-compute myTemp mobile temp/eff 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -nuclei and electrons in the electron force field -model. A compute of this style can be used by commands that compute a -temperature, e.g. thermo_modify, fix -npt/eff, etc. -

    -

    The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for -nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s -includes the radial electron velocity contributions), dim = 2 or 3 = -dimensionality of the simulation, N = number of atoms (only total -number of nuclei in the eFF (see the pair_eff -command) in the group, k = Boltzmann constant, and T = temperature. -This expression is summed over all nuclear and electronic degrees of -freedom, essentially by setting the kinetic contribution to the heat -capacity to 3/2k (where only nuclei contribute). This subtlety is -valid for temperatures well below the Fermi temperature, which for -densities two to five times the density of liquid H2 ranges from -86,000 to 170,000 K. -

    -

    IMPORTANT NOTE: For eFF models, in order to override the default -temperature reported by LAMMPS in the thermodynamic quantities -reported via the thermo command, the user should apply a -thermo_modify command, as shown in the following -example: -

    -
    compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press 
-thermo_modify   temp effTemp 
-
    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. For the eFF, -again, the radial electronic velocities are also considered. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    Output info: -

    -

    The scalar value calculated by this compute is "intensive", meaning it -is independent of the number of atoms in the simulation. The vector -values are "extensive", meaning they scale with the number of atoms in -the simulation. -

    -

    Restrictions: -

    -

    This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute temp/partial, compute -temp/region, compute -pressure -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_partial.html b/doc/doc2/compute_temp_partial.html deleted file mode 100644 index 8a59108641..0000000000 --- a/doc/doc2/compute_temp_partial.html +++ /dev/null @@ -1,127 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/partial command -

    -

    compute temp/partial/cuda command -

    -

    Syntax: -

    -
    compute ID group-ID temp/partial xflag yflag zflag 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/partial = style name of this compute command -
    • xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension -
    -

    Examples: -

    -
    compute newT flow temp/partial 1 1 0 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms, after excluding one or more velocity components. A compute of -this style can be used by any command that computes a temperature, -e.g. thermo_modify, fix -temp/rescale, fix npt, etc. -

    -

    The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = dimensionality of the simulation, N = number of atoms in the -group, k = Boltzmann constant, and T = temperature. The calculation -of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = -0. The dim parameter is adjusted to give the correct number of -degrees of freedom. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the calculation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    The removal of velocity components by this fix is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. If this compute is used with a fix command -that performs thermostatting then this bias will be subtracted from -each atom, thermostatting of the remaining thermal velocity will be -performed, and the bias will be added back in. Thermostatting fixes -that work in this way include fix nvt, fix -temp/rescale, fix -temp/berendsen, and fix -langevin. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp, compute -temp/region, compute -pressure -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_profile.html b/doc/doc2/compute_temp_profile.html deleted file mode 100644 index 1312ae63e6..0000000000 --- a/doc/doc2/compute_temp_profile.html +++ /dev/null @@ -1,195 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/profile command -

    -

    Syntax: -

    -
    compute ID group-ID temp/profile xflag yflag zflag binstyle args 
-
    -
    • ID, group-ID are documented in compute command - -
    • temp/profile = style name of this compute command - -
    • xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension - -
    • binstyle = x or y or z or xy or yz or xz or xyz - -
        x arg = Nx
-  y arg = Ny
-  z arg = Nz
-  xy args = Nx Ny
-  yz args = Ny Nz
-  xz args = Nx Nz
-  xyz args = Nx Ny Nz
-    Nx,Ny,Nz = number of velocity bins in x,y,z dimensions 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = out - -
        out value = tensor or bin 
-
      - -
    -

    Examples: -

    -
    compute myTemp flow temp/profile 1 1 1 x 10
-compute myTemp flow temp/profile 1 1 1 x 10 out bin
-compute myTemp flow temp/profile 0 1 1 xyz 20 20 20 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms, after subtracting out a spatially-averaged center-of-mass -velocity field, before computing the kinetic energy. This can be -useful for thermostatting a collection of atoms undergoing a complex -flow, e.g. via a profile-unbiased thermostat (PUT) as described in -(Evans). A compute of this style can be used by any command -that computes a temperature, e.g. thermo_modify, -fix temp/rescale, fix npt, etc. -

    -

    The xflag, yflag, zflag settings determine which components of -average velocity are subtracted out. -

    -

    The binstyle setting and its Nx, Ny, Nz arguments determine -how bins are setup to perform spatial averaging. "Bins" can be 1d -slabs, 2d pencils, or 3d bricks depending on which binstyle is used. -The simulation box is partitioned conceptually into Nx by Ny by -Nz bins. Depending on the binstyle, you may only specify one or -two of these values; the others are effectively set to 1 (no binning -in that dimension). For non-orthogonal (triclinic) simulation boxes, -the bins are "tilted" slabs or pencils or bricks that are parallel to -the tilted faces of the box. See the region prism -command for a discussion of the geometry of tilted boxes in LAMMPS. -

    -

    When a temperature is computed, the center-of-mass velocity for the -set of atoms that are both in the compute group and in the same -spatial bin is calculated. This bias velocity is then subtracted from -the velocities of individual atoms in the bin to yield a thermal -velocity for each atom. Note that if there is only one atom in the -bin, its thermal velocity will thus be 0.0. -

    -

    After the spatially-averaged velocity field has been subtracted from -each atom, the temperature is calculated by the formula KE = (dim/2 N -- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of -atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the -simulation, N = number of atoms in the group, k = Boltzmann constant, -and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom -subtracted to adjust for the removal of the center-of-mass velocity in -each of Nx*Ny*Nz bins, as discussed in the (Evans) paper. -

    -

    If the out keyword is used with a tensor value, which is the -default, a kinetic energy tensor, stored as a 6-element vector, is -also calculated by this compute for use in the computation of a -pressure tensor. The formula for the components of the tensor is the -same as the above formula, except that v^2 is replaced by vx*vy for -the xy component, etc. The 6 components of the vector are ordered xx, -yy, zz, xy, xz, yz. -

    -

    If the out keyword is used with a bin value, the count of atoms -and computed temperature for each bin are stored for output, as an -array of values, as described below. The temperature of each bin is -calculated as described above, where the bias velocity is subtracted -and only the remaining thermal velocity of atoms in the bin -contributes to the temperature. See the note below for how the -temperature is normalized by the degrees-of-freedom of atoms in the -bin. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    The removal of the spatially-averaged velocity field by this fix is -essentially computing the temperature after a "bias" has been removed -from the velocity of the atoms. If this compute is used with a fix -command that performs thermostatting then this bias will be subtracted -from each atom, thermostatting of the remaining thermal velocity will -be performed, and the bias will be added back in. Thermostatting -fixes that work in this way include fix nvt, fix -temp/rescale, fix -temp/berendsen, and fix -langevin. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    IMPORTANT NOTE: When using the out keyword with a value of bin, -the calculated temperature for each bin does not include the -degrees-of-freedom adjustment described in the preceeding paragraph, -for fixes that constrain molecular motion. It does include the -adjustment due to the extra option, which is applied to each bin. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. Using this compute in conjunction with a -thermostatting fix, as explained there, will effectively implement a -profile-unbiased thermostat (PUT), as described in (Evans). -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature). Depending -on the setting of the out keyword, it also calculates a global -vector or array. For out = tensor, it calculates a vector of -length 6 (KE tensor), which can be accessed by indices 1-6. For out -= bin it calculates a global array which has 2 columns and N rows, -where N is the number of bins. The first column contains the number -of atoms in that bin. The second contains the temperature of that -bin, calculated as described above. The ordering of rows in the array -is as follows. Bins in x vary fastest, then y, then z. Thus for a -10x10x10 3d array of bins, there will be 1000 rows. The bin with -indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10 -+ ix = 322, where the rows are numbered from 1 to 1000 and the bin -indices are numbered from 1 to 10 in each dimension. -

    -

    These values can be used by any command that uses global scalar or -vector or array values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". The array values are "intensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. The first column -of array values are counts; the values in the second column will be in -temperature units. -

    -

    Restrictions: -

    -

    You should not use too large a velocity-binning grid, especially in -3d. In the current implementation, the binned velocity averages are -summed across all processors, so this will be inefficient if the grid -is too large, and the operation is performed every timestep, as it -will be for most thermostats. -

    -

    Related commands: -

    -

    compute temp, compute -temp/ramp, compute -temp/deform, compute -pressure -

    -

    Default: -

    -

    The option default is out = tensor. -

    -
    - - - -

    (Evans) Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986). -

    - diff --git a/doc/doc2/compute_temp_ramp.html b/doc/doc2/compute_temp_ramp.html deleted file mode 100644 index 686ad9cd61..0000000000 --- a/doc/doc2/compute_temp_ramp.html +++ /dev/null @@ -1,122 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/ramp command -

    -

    Syntax: -

    -
    compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ... 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/ramp = style name of this compute command -
    • vdim = vx or vy or vz -
    • vlo,vhi = subtract velocities between vlo and vhi (velocity units) -
    • dim = x or y or z -
    • clo,chi = lower and upper bound of domain to subtract from (distance units) -
    • zero or more keyword/value pairs may be appended -
    • keyword = units -
    -
      units value = lattice or box 
-
    -

    Examples: -

    -
    compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms, after subtracting out an ramped velocity profile before -computing the kinetic energy. A compute of this style can be used by -any command that computes a temperature, -e.g. thermo_modify, fix -temp/rescale, fix npt, etc. -

    -

    The meaning of the arguments for this command which define the -velocity ramp are the same as for the velocity ramp -command which was presumably used to impose the velocity. -

    -

    After the ramp velocity has been subtracted from the specified -dimension for each atom, the temperature is calculated by the formula -KE = dim/2 N k T, where KE = total kinetic energy of the group of -atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the -simulation, N = number of atoms in the group, k = Boltzmann constant, -and T = temperature. -

    -

    The units keyword determines the meaning of the distance units used -for coordinates (c1,c2) and velocities (vlo,vhi). A box value -selects standard distance units as defined by the units -command, e.g. Angstroms for units = real or metal. A lattice value -means the distance units are in lattice spacings; e.g. velocity = -lattice spacings / tau. The lattice command must have -been previously used to define the lattice spacing. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    The removal of the ramped velocity component by this fix is -essentially computing the temperature after a "bias" has been removed -from the velocity of the atoms. If this compute is used with a fix -command that performs thermostatting then this bias will be subtracted -from each atom, thermostatting of the remaining thermal velocity will -be performed, and the bias will be added back in. Thermostatting -fixes that work in this way include fix nvt, fix -temp/rescale, fix -temp/berendsen, and fix -langevin. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp, compute -temp/profie, compute -temp/deform, compute -pressure -

    -

    Default: -

    -

    The option default is units = lattice. -

    - diff --git a/doc/doc2/compute_temp_region.html b/doc/doc2/compute_temp_region.html deleted file mode 100644 index f3fa62c9ed..0000000000 --- a/doc/doc2/compute_temp_region.html +++ /dev/null @@ -1,115 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/region command -

    -

    Syntax: -

    -
    compute ID group-ID temp/region region-ID 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/region = style name of this compute command -
    • region-ID = ID of region to use for choosing atoms -
    -

    Examples: -

    -
    compute mine flow temp/region boundary 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms in a geometric region. This can be useful for thermostatting -one portion of the simulation box. E.g. a McDLT simulation where one -side is cooled, and the other side is heated. A compute of this style -can be used by any command that computes a temperature, -e.g. thermo_modify, fix -temp/rescale, etc. -

    -

    Note that a region-style temperature can be used to thermostat with -fix temp/rescale or fix -langevin, but should probably not be used with -Nose/Hoover style fixes (fix nvt, fix -npt, or fix nph), if the -degrees-of-freedom included in the computed T varies with time. -

    -

    The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in both the group and region, k = Boltzmann constant, and T = -temperature. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is calculated each -time the temperature is evaluated since it is assumed atoms can -enter/leave the region. Thus there is no need to use the dynamic -option of the compute_modify command for this -compute style. -

    -

    The removal of atoms outside the region by this fix is essentially -computing the temperature after a "bias" has been removed, which in -this case is the velocity of any atoms outside the region. If this -compute is used with a fix command that performs thermostatting then -this bias will be subtracted from each atom, thermostatting of the -remaining thermal velocity will be performed, and the bias will be -added back in. Thermostatting fixes that work in this way include -fix nvt, fix temp/rescale, fix -temp/berendsen, and fix -langevin. This means that when this compute -is used to calculate the temperature for any of the thermostatting -fixes via the fix modify temp command, the thermostat -will operate only on atoms that are currently in the geometric -region. -

    -

    Unlike other compute styles that calculate temperature, this compute -does not subtract out degrees-of-freedom due to fixes that constrain -motion, such as fix shake and fix -rigid. This is because those degrees of freedom -(e.g. a constrained bond) could apply to sets of atoms that straddle -the region boundary, and hence the concept is somewhat ill-defined. -If needed the number of subtracted degrees-of-freedom can be set -explicitly using the extra option of the -compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp, compute -pressure -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_region_eff.html b/doc/doc2/compute_temp_region_eff.html deleted file mode 100644 index e4e84b9e8c..0000000000 --- a/doc/doc2/compute_temp_region_eff.html +++ /dev/null @@ -1,69 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/region/eff command -

    -

    Syntax: -

    -
    compute ID group-ID temp/region/eff region-ID 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/region/eff = style name of this compute command -
    • region-ID = ID of region to use for choosing atoms -
    -

    Examples: -

    -
    compute mine flow temp/region/eff boundary 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -nuclei and electrons in the electron force field -model, within a geometric region using the electron force field. A -compute of this style can be used by commands that compute a -temperature, e.g. thermo_modify. -

    -

    The operation of this compute is exactly like that described by the -compute temp/region command, except that -the formula for the temperature itself includes the radial electron -velocity contributions, as discussed by the compute -temp/eff command. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute temp/region, compute -temp/eff, compute -pressure -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_rotate.html b/doc/doc2/compute_temp_rotate.html deleted file mode 100644 index cbd3a31042..0000000000 --- a/doc/doc2/compute_temp_rotate.html +++ /dev/null @@ -1,101 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/rotate command -

    -

    Syntax: -

    -
    compute ID group-ID temp/rotate 
-
    -
    • ID, group-ID are documented in compute command -
    • temp/rotate = style name of this compute command -
    -

    Examples: -

    -
    compute Tbead bead temp/rotate 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -atoms, after subtracting out the center-of-mass velocity and angular velocity of the group. -This is useful if the group is expected to have a non-zero net -velocity and/or global rotation motion for some reason. A compute of this style can be used by any -command that computes a temperature, -e.g. thermo_modify, fix -temp/rescale, fix npt, etc. -

    -

    After the center-of-mass velocity and angular velocity has been subtracted from each atom, -the temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    The removal of the center-of-mass velocity and angular velocity by this fix is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. If this compute is used with a fix command -that performs thermostatting then this bias will be subtracted from -each atom, thermostatting of the remaining thermal velocity will be -performed, and the bias will be added back in. Thermostatting fixes -that work in this way include fix nvt, fix -temp/rescale, fix -temp/berendsen, and fix -langevin. -

    -

    This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as fix shake and -fix rigid. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -extra option of the compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute temp -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_temp_sphere.html b/doc/doc2/compute_temp_sphere.html deleted file mode 100644 index dcbfd9a28a..0000000000 --- a/doc/doc2/compute_temp_sphere.html +++ /dev/null @@ -1,147 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute temp/sphere command -

    -

    Syntax: -

    -
    compute ID group-ID temp/sphere keyword value ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • temp/sphere = style name of this compute command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = bias or dof - -
        bias value = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias
-  dof value = all or rotate
-    all = compute temperature of translational and rotational degrees of freedom
-    rotate = compute temperature of just rotational degrees of freedom 
-
      - -
    -

    Examples: -

    -
    compute 1 all temp/sphere
-compute myTemp mobile temp/sphere bias tempCOM
-compute myTemp mobile temp/sphere dof rotate 
-
    -

    Description: -

    -

    Define a computation that calculates the temperature of a group of -spherical particles, including a contribution from both their -translational and rotational kinetic energy. This differs from the -usual compute temp command, which assumes point -particles with only translational kinetic energy. -

    -

    Both point and finite-size particles can be included in the group. -Point particles do not rotate, so they have only 3 translational -degrees of freedom. For 3d spherical particles, each has 6 degrees of -freedom (3 translational, 3 rotational). For 2d spherical particles, -each has 3 degrees of freedom (2 translational, 1 rotational). -

    -

    IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that -all finite-size spherical particles in your model will freely rotate, -sampling all their rotational dof. It is possible to use a -combination of interaction potentials and fixes that induce no torque -or otherwise constrain some of all of your particles so that this is -not the case. Then there are less dof and you should use the -compute_modify extra command to adjust the dof -accordingly. -

    -

    The translational kinetic energy is computed the same as is described -by the compute temp command. The rotational -kinetic energy is computed as 1/2 I w^2, where I is the moment of -inertia for a sphere and w is the particle's angular velocity. -

    -

    IMPORTANT NOTE: For 2d models, particles are treated -as spheres, not disks, meaning their moment of inertia will be the -same as in 3d. -

    -

    A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute. The formula for the components of the -tensor is the same as the above formulas, except that v^2 and w^2 are -replaced by vx*vy and wx*wy for the xy component. The 6 components of -the vector are ordered xx, yy, zz, xy, xz, yz. -

    -

    The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the dynamic option of the -compute_modify command if this is not the case. -

    -

    This compute subtracts out translational degrees-of-freedom due to -fixes that constrain molecular motion, such as fix -shake and fix rigid. This means the -temperature of groups of atoms that include these constraints will be -computed correctly. If needed, the subtracted degrees-of-freedom can -be altered using the extra option of the -compute_modify command. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -
    - -

    The keyword/value option pairs are used in the following ways. -

    -

    For the bias keyword, bias-ID refers to the ID of a temperature -compute that removes a "bias" velocity from each atom. This allows -compute temp/sphere to compute its thermal temperature after the -translational kinetic energy components have been altered in a -prescribed way, e.g. to remove a flow velocity profile. Thermostats -that use this compute will work with this bias term. See the doc -pages for individual computes that calculate a temperature and the doc -pages for fixes that perform thermostatting for more details. -

    -

    For the dof keyword, a setting of all calculates a temperature -that includes both translational and rotational degrees of freedom. A -setting of rotate calculates a temperature that includes only -rotational degrees of freedom. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "intensive". The -vector values are "extensive". -

    -

    The scalar value will be in temperature units. The -vector values will be in energy units. -

    -

    Restrictions: -

    -

    This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the atom_style sphere -command. -

    -

    All particles in the group must be finite-size spheres, or point -particles with radius = 0.0. -

    -

    Related commands: -

    -

    compute temp, compute -temp/asphere -

    -

    Default: -

    -

    The option defaults are no bias and dof = all. -

    - diff --git a/doc/doc2/compute_ti.html b/doc/doc2/compute_ti.html deleted file mode 100644 index 5a7ef6e1ed..0000000000 --- a/doc/doc2/compute_ti.html +++ /dev/null @@ -1,148 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute ti command -

    -

    Syntax: -

    -
    compute ID group ti keyword args ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • ti = style name of this compute command - -
    • one or more attribute/arg pairs may be appended - -
    • keyword = pair style (lj/cut, gauss, born, etc) or tail or kspace - -
        pair style args = atype v_name1 v_name2
-    atype = atom type (see asterisk form below)
-    v_name1 = variable with name1 that is energy scale factor and function of lambda
-    v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
-  tail args = atype v_name1 v_name2
-    atype = atom type (see asterisk form below)
-    v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
-    v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
-  kspace args = atype v_name1 v_name2
-    atype = atom type (see asterisk form below)
-    v_name1 = variable with name1 that is K-Space scale factor and function of lambda
-    v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda 
-
      - -
    -

    Examples: -

    -
    compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
-compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks 
-
    -

    Description: -

    -

    Define a computation that calculates the derivative of the interaction -potential with respect to lambda, the coupling parameter used in a -thermodynamic integration. This derivative can be used to infer a -free energy difference resulting from an alchemical simulation, as -described in Eike. -

    -

    Typically this compute will be used in conjunction with the fix -adapt command which can perform alchemical -transformations by adusting the strength of an interaction potential -as a simulation runs, as defined by one or more -pair_style or kspace_style -commands. This scaling is done via a prefactor on the energy, forces, -virial calculated by the pair or K-Space style. The prefactor is -often a function of a lambda parameter which may be adjusted from 0 -to 1 (or vice versa) over the course of a run. The -time-dependent adjustment is what the fix adapt -command does. -

    -

    Assume that the unscaled energy of a pair_style or kspace_style is -given by U. Then the scaled energy is -

    -
    Us = f(lambda) U 
-
    -

    where f() is some function of lambda. What this compute calculates is -

    -
    dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda 
-
    -

    which is the derivative of the system's scaled potential energy Us -with respect to lambda. -

    -

    To perform this calculation, you provide one or more atom types as -atype. Atype can be specified in one of two ways. An explicit -numeric values can be used, as in the 1st example above. Or a -wildcard asterisk can be used in place of or in conjunction with the -atype argument to select multiple atom types. This takes the form -"*" or "*n" or "n*" or "m*n". If N = the number of atom types, then -an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). -

    -

    You also specify two functions, as equal-style -variables. The first is specified as v_name1, where -name1 is the name of the variable, and is f(lambda) in the notation -above. The second is specified as v_name2, where name2 is the -name of the variable, and is df(lambda) / dlambda in the notation -above. I.e. it is the analytic derivative of f() with respect to -lambda. Note that the name1 variable is also typically given as an -argument to the fix adapt command. -

    -

    An alchemical simulation may use several pair potentials together, -invoked via the pair_style hybrid or hybrid/overlay -command. The total dUs/dlambda for the overall system is calculated -as the sum of each contributing term as listed by the keywords in the -compute ti command. Individual pair potentials can be listed, which -will be sub-styles in the hybrid case. You can also include a K-space -term via the kspace keyword. You can also include a pairwise -long-range tail correction to the energy via the tail keyword. -

    -

    For each term you can specify a different (or the same) scale factor -by the two variables that you list. Again, these will typically -correspond toe the scale factors applied to these various potentials -and the K-Space contribution via the fix_adapt -command. -

    -

    More details about the exact functional forms for the computation of -du/dl can be found in the paper by Eike. -

    -
    - -

    Output info: -

    -

    This compute calculates a global scalar, namely dUs/dlambda. This -value can be used by any command that uses a global scalar value from -a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The scalar value calculated by this compute is "extensive". -

    -

    The scalar value will be in energy units. -

    -

    Restrictions: -

    -

    This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix adapt -

    -

    Default: none -

    -
    - - - -

    (Eike) Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006). -

    - diff --git a/doc/doc2/compute_torque_chunk.html b/doc/doc2/compute_torque_chunk.html deleted file mode 100644 index 593397646d..0000000000 --- a/doc/doc2/compute_torque_chunk.html +++ /dev/null @@ -1,92 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute torque/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID torque/chunk chunkID 
-
    -
    • ID, group-ID are documented in compute command -
    • torque/chunk = style name of this compute command -
    • chunkID = ID of compute chunk/atom command -
    -

    Examples: -

    -
    compute 1 fluid torque/chunk molchunk 
-
    -

    Description: -

    -

    Define a computation that calculates the torque on multiple chunks of -atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates the 3 components of the torque vector for eqch -chunk, due to the forces on the individual atoms in the chunk around -the center-of-mass of the chunk. The calculation includes all effects -due to atoms passing thru periodic boundaries. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's -torque in "unwrapped" form, by using the image flags associated with -each atom. See the dump custom command for a discussion -of "unwrapped" coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -

    -

    The simplest way to output the results of the compute torque/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all torque/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array where the number of rows = the -number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The number of columns = -3 for the 3 xyz components of the torque for each chunk. These values -can be accessed by any command that uses global array values from a -compute as input. See Section_howto 15 -for an overview of LAMMPS output options. -

    -

    The array values are "intensive". The array values will be in -force-distance units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    variable torque() function -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_vacf.html b/doc/doc2/compute_vacf.html deleted file mode 100644 index 12a3411eec..0000000000 --- a/doc/doc2/compute_vacf.html +++ /dev/null @@ -1,76 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute vacf command -

    -

    Syntax: -

    -
    compute ID group-ID vacf 
-
    -
    • ID, group-ID are documented in compute command -
    • vacf = style name of this compute command -
    -

    Examples: -

    -
    compute 1 all vacf
-compute 1 upper vacf 
-
    -

    Description: -

    -

    Define a computation that calculates the velocity auto-correlation -function (VACF), averaged over a group of atoms. Each atom's -contribution to the VACF is its current velocity vector dotted into -its initial velocity vector at the time the compute was specified. -

    -

    A vector of four quantites is calculated by this compute. The first 3 -elements of the vector are vx * vx0 (and similarly for the y and z -components), summed and averaged over atoms in the group. Vx is the -current x-component of velocity for the atom, vx0 is the initial -x-component of velocity for the atom. The 4th element of the vector -is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and -averaged over atoms in the group. -

    -

    The integral of the VACF versus time is proportional to the diffusion -coefficient of the diffusing atoms. This can be computed in the -following manner, using the variable trap() function: -

    -
    compute         2 all vacf
-fix             5 all vector 1 c_2[4]
-variable        diff equal dt*trap(f_5)
-thermo_style    custom step v_diff 
-
    -

    IMPORTANT NOTE: If you want the quantities calculated by this compute -to be continuous when running from a restart file, -then you should use the same ID for this compute, as in the original -run. This is so that the fix this compute creates to store per-atom -quantities will also have the same ID, and thus be initialized -correctly with time=0 atom velocities from the restart file. -

    -

    Output info: -

    -

    This compute calculates a global vector of length 4, which can be -accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See this -section for an overview of LAMMPS output -options. -

    -

    The vector values are "intensive". The vector values will be in -velocity^2 units. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute msd -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_vcm_chunk.html b/doc/doc2/compute_vcm_chunk.html deleted file mode 100644 index 8c23af9a58..0000000000 --- a/doc/doc2/compute_vcm_chunk.html +++ /dev/null @@ -1,82 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute vcm/chunk command -

    -

    Syntax: -

    -
    compute ID group-ID vcm/chunk chunkID 
-
    -
    • ID, group-ID are documented in compute command -
    • vcm/chunk = style name of this compute command -
    • chunkID = ID of compute chunk/atom command -
    -

    Examples: -

    -
    compute 1 fluid vcm/chunk molchunk 
-
    -

    Description: -

    -

    Define a computation that calculates the center-of-mass velocity for -multiple chunks of atoms. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    This compute calculates the x,y,z components of the center-of-mass -velocity for each chunk. This is done by summing mass*velocity for -each atom in the chunk and dividing the sum by the total mass of the -chunk. -

    -

    Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. -

    -

    The simplest way to output the results of the compute vcm/chunk -calculation to a file is to use the fix ave/time -command, for example: -

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all vcm/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector 
-
    -

    Output info: -

    -

    This compute calculates a global array where the number of rows = the -number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The number of columns = -3 for the x,y,z center-of-mass velocity coordinates of each chunk. -These values can be accessed by any command that uses global array -values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The array values are "intensive". The array values will be in -velocity units. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_voronoi_atom.html b/doc/doc2/compute_voronoi_atom.html deleted file mode 100644 index ea7f0fb50c..0000000000 --- a/doc/doc2/compute_voronoi_atom.html +++ /dev/null @@ -1,183 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute voronoi/atom command -

    -

    Syntax: -

    -
    compute ID group-ID voronoi/atom keyword arg ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • voronoi/atom = style name of this compute command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = only_group or surface or radius or edge_histo or edge_threshold or face_threshold - -
        only_group = no arg
-  occupation = no arg
-  surface arg = sgroup-ID
-    sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
-      this keyword adds a third column to the compute output
-  radius arg = v_r
-    v_r = radius atom style variable for a poly-disperse Voronoi tessellation
-  edge_histo arg = maxedge
-    maxedge = maximum number of Voronoi cell edges to be accounted in the histogram 
-  edge_threshold arg = minlength
-    minlength = minimum length for an edge to be counted
-  face_threshold arg = minarea
-    minarea = minimum area for a face to be counted 
-
      - -
    -

    Examples: -

    -
    compute 1 all voronoi/atom
-compute 2 precipitate voronoi/atom surface matrix
-compute 3b precipitate voronoi/atom radius v_r 
-compute 4 solute voronoi/atom only_group 
-
    -
    compute 5 defects voronoi/atom occupation 
-
    -

    Description: -

    -

    Define a computation that calculates the Voronoi tessellation of the -atoms in the simulation box. The tessellation is calculated using all -atoms in the simulation, but non-zero values are only stored for atoms -in the group. -

    -

    By default two quantities per atom are calculated by this compute. -The first is the volume of the Voronoi cell around each atom. Any -point in an atom's Voronoi cell is closer to that atom than any other. -The second is the number of faces of the Voronoi cell, which is also -the number of nearest neighbors of the atom in the middle of the cell. -

    -
    - -

    If the only_group keyword is specified the tessellation is performed -only with respect to the atoms contained in the compute group. This is -equivalent to deleting all atoms not contained in the group prior to -evaluating the tessellation. -

    -

    If the surface keyword is specified a third quantity per atom is -computed: the Voronoi cell surface of the given atom. surface takes -a group ID as an argument. If a group other than all is specified, -only the Voronoi cell facets facing a neighbor atom from the specified -group are counted towards the surface area. -

    -

    In the example above, a precipitate embedded in a matrix, only atoms -at the surface of the precipitate will have non-zero surface area, and -only the outward facing facets of the Voronoi cells are counted (the -hull of the precipitate). The total surface area of the precipitate -can be obtained by running a "reduce sum" compute on c_2[3] -

    -

    If the radius keyword is specified with an atom style variable as -the argument, a poly-disperse Voronoi tessellation is -performed. Examples for radius variables are -

    -
    variable r1 atom (type==1)*0.1+(type==2)*0.4
-compute radius all property/atom radius
-variable r2 atom c_radius 
-
    -

    Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms -and 0.4 units for type 2 atoms, and v_r2 accesses the radius property -present in atom_style sphere for granular models. -

    -

    The edge_histo keyword activates the compilation of a histogram of -number of edges on the faces of the Voronoi cells in the compute -group. The argument maxedge of the this keyword is the largest number -of edges on a single Voronoi cell face expected to occur in the -sample. This keyword adds the generation of a global vector with -maxedge+1 entries. The last entry in the vector contains the number of -faces with with more than maxedge edges. Since the polygon with the -smallest amount of edges is a triangle, entries 1 and 2 of the vector -will always be zero. -

    -

    The edge_threshold and face_threshold keywords allow the -suppression of edges below a given minimum length and faces below a -given minimum area. Ultra short edges and ultra small faces can occur -as artifacts of the Voronoi tessellation. These keywords will affect -the neighbor count and edge histogram outputs. -

    -

    If the occupation keyword is specified the tessellation is only -performed for the first invocation of the compute and then stored. -For all following invocations of the compute the number of atoms in -each Voronoi cell in the stored tessellation is counted. In this mode -the compute returns a per-atom array with 2 columns. The first column -is the number of atoms currently in the Voronoi volume defined by this -atom at the time of the first invocation of the compute (note that the -atom may have moved significantly). The second column contains the -total number of atoms sharing the Voronoi cell of the stored -tessellation at the location of the current atom. Numbers in column -one can be any positive integer including zero, while column two -values will always be greater than zero. Column one data can be used -to locate vacancies (the coordinates are given by the atom coordinates -at the time step when the compute was first invoked), while column two -data can be used to identify interstitial atoms. -

    -
    - -

    The Voronoi calculation is performed by the freely available Voro++ -package, written by Chris Rycroft at UC Berkeley and LBL, -which must be installed on your system when building LAMMPS for use -with this compute. See instructions on obtaining and installing the -Voro++ software in the src/VORONOI/README file. -

    - - -

    IMPORTANT NOTE: The calculation of Voronoi volumes is performed by -each processor for the atoms it owns, and includes the effect of ghost -atoms stored by the processor. This assumes that the Voronoi cells of -owned atoms are not affected by atoms beyond the ghost atom cut-off -distance. This is usually a good assumption for liquid and solid -systems, but may lead to underestimation of Voronoi volumes in low -density systems. By default, the set of ghost atoms stored by each -processor is determined by the cutoff used for -pair_style interactions. The cutoff can be set -explicitly via the comm_modify cutoff command. -

    -

    IMPORTANT NOTE: The Voro++ package performs its calculation in 3d. -This should still work for a 2d LAMMPS simulation, to effectively -compute Voronoi "areas", so long as the z-dimension of the box is -roughly the same (or smaller) compared to the separation of the atoms. -Typical values for the z box dimensions in a 2d LAMMPS model are -0.5 -to 0.5, which satisfies the criterion for most units -systems. Note that you define the z extent of the simulation box for -2d simulations when using the create_box or -read_data commands. -

    -

    Output info: -

    -

    This compute calculates a per-atom array with 2 columns. In regular -dynamic tessellation mode the first column is the Voronoi volume, the -second is the neighbor count, as described above (read above for the -output data in case the occupation keyword is specified). -These values can be accessed by any command that -uses per-atom values from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -

    -

    The Voronoi cell volume will be in distance units cubed. -

    -

    Restrictions: -

    -

    This compute is part of the VORONOI package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    dump custom -

    -

    Default: none -

    - diff --git a/doc/doc2/compute_xrd.html b/doc/doc2/compute_xrd.html deleted file mode 100644 index cb2786306c..0000000000 --- a/doc/doc2/compute_xrd.html +++ /dev/null @@ -1,214 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    compute xrd command -

    -

    Syntax: -

    -
    compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ... 
-
    -
    • ID, group-ID are documented in compute command - -
    • xrd = style name of this compute command - -
    • lambda = wavelength of incident radiation (length units) - -
    • type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = 2Theta or c or LP or manual or echo - -
        2Theta values = Min2Theta Max2Theta
-    Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore 
-    (radians or degrees)
-  c values = c1 c2 c3
-    c1,c2,c3 = parameters to adjust the spacing of the reciprocal 
-               lattice nodes in the h, k, and l directions respectively
-  LP value = switch to apply Lorentz-polarization factor
-    0/1 = off/on
-  manual = flag to use manual spacing of reciprocal lattice points 
-             based on the values of the c parameters 
-  echo = flag to provide extra output for debugging purposes 
-
      - -
    -

    Examples: -

    -
    compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo 
-compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual 
-
    -
    fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
-fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd 
-
    -
    -
    -

    Description: -

    -

    Define a computation that calculates x-ray diffraction intensity as described -in (Coleman) on a mesh of reciprocal lattice nodes defined -by the entire simulation domain (or manually) using a simulated radiation -of wavelength lambda. -

    -

    The x-ray diffraction intensity, I, at each reciprocal lattice point, k, -is computed from the structure factor, F, using the equations: -

    -
    -
    -
    -
    -
    -
    -
    -
    -

    Here, K is the location of the reciprocal lattice node, rj is the -position of each atom, fj are atomic scattering factors, LP is the -Lorentz-polarization factor, and theta is the scattering angle of -diffraction. The Lorentz-polarization factor can be turned off using -the optional LP keyword. -

    -

    Diffraction intensities are calculated on a three-dimensional mesh of -reciprocal lattice nodes. The mesh spacing is defined either (a) -by the entire simulation domain or (b) manually using selected values as -shown in the 2D diagram below. -

    -
    -
    -

    For a mesh defined by the simulation domain, a rectilinear grid is -constructed with spacing c*inv(A) along each reciprocal lattice -axis. Where A are the vectors corresponding to the edges of the -simulation cell. If one or two directions has non-periodic boundary -conditions, then the spacing in these directions is defined from the -average of the (inversed) box lengths with periodic boundary conditions. -Meshes defined by the simulation domain must contain at least one periodic -boundary. -

    -

    If the manual flag is included, the mesh of reciprocal lattice nodes -will defined using the c values for the spacing along each -reciprocal lattice axis. Note that manual mapping of the reciprocal -space mesh is good for comparing diffraction results from multiple -simulations; however it can reduce the likelihood that Bragg -reflections will be satisfied unless small spacing parameters (< 0.05 -Angstrom^(-1)) are implemented. Meshes with manual spacing do not -require a periodic boundary. -

    -

    The limits of the reciprocal lattice mesh are determined by range of -scattering angles explored. The 2Theta parameters allows the user -to reduce the scattering angle range to only the region of interest -which reduces the cost of the computation. -

    -

    The atomic scattering factors, fj, accounts for the reduction in -diffraction intensity due to Compton scattering. Compute xrd uses -analytical approximations of the atomic scattering factors that vary -for each atom type (type1 type2 ... typeN) and angle of diffraction. -The analytic approximation is computed using the formula -(Colliex): -

    -
    -
    -

    Coefficients parameterized by (Peng) are assigned for each -atom type designating the chemical symbol and charge of each atom -type. Valid chemical symbols for compute xrd are: -

    -

    H: He1-: He: Li: Li1+: - Be: Be2+: B: C: Cval: - N: O: O1-: F: F1-: - Ne: Na: Na1+: Mg: Mg2+: - Al: Al3+: Si: Sival: Si4+: - P: S: Cl: Cl1-: Ar: - K: Ca: Ca2+: Sc: Sc3+: - Ti: Ti2+: Ti3+: Ti4+: V: - V2+: V3+: V5+: Cr: Cr2+: - Cr3+: Mn: Mn2+: Mn3+: Mn4+: - Fe: Fe2+: Fe3+: Co: Co2+: - Co: Ni: Ni2+: Ni3+: Cu: - Cu1+: Cu2+: Zn: Zn2+: Ga: - Ga3+: Ge: Ge4+: As: Se: - Br: Br1-: Kr: Rb: Rb1+: - Sr: Sr2+: Y: Y3+: Zr: - Zr4+: Nb: Nb3+: Nb5+: Mo: - Mo3+: Mo5+: Mo6+: Tc: Ru: - Ru3+: Ru4+: Rh: Rh3+: Rh4+: - Pd: Pd2+: Pd4+: Ag: Ag1+: - Ag2+: Cd: Cd2+: In: In3+: - Sn: Sn2+: Sn4+: Sb: Sb3+: - Sb5+: Te: I: I1-: Xe: - Cs: Cs1+: Ba: Ba2+: La: - La3+: Ce: Ce3+: Ce4+: Pr: - Pr3+: Pr4+: Nd: Nd3+: Pm: - Pm3+: Sm: Sm3+: Eu: Eu2+: - Eu3+: Gd: Gd3+: Tb: Tb3+: - Dy: Dy3+: Ho: Ho3+: Er: - Er3+: Tm: Tm3+: Yb: Yb2+: - Yb3+: Lu: Lu3+: Hf: Hf4+: - Ta: Ta5+: W: W6+: Re: - Os: Os4+: Ir: Ir3+: Ir4+: - Pt: Pt2+: Pt4+: Au: Au1+: - Au3+: Hg: Hg1+: Hg2+: Tl: - Tl1+: Tl3+: Pb: Pb2+: Pb4+: - Bi: Bi3+: Bi5+: Po: At: - Rn: Fr: Ra: Ra2+: Ac: - Ac3+: Th: Th4+: Pa: U: - U3+: U4+: U6+: Np: Np3+: - Np4+: Np6+: Pu: Pu3+: Pu4+: - Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:) -

    -

    If the echo keyword is specified, compute xrd will provide extra -reporting information to the screen. -

    -

    Output info: -

    -

    This compute calculates a global array. The number of rows in the -array is the number of reciprocal lattice nodes that are explored -which by the mesh. The global array has 2 columns. -

    -

    The first column contains the diffraction angle in the units (radians -or degrees) provided with the 2Theta values. The second column contains -the computed diffraction intensities as described above. -

    -

    The array can be accessed by any command that uses global values -from a compute as input. See this section for an overview of LAMMPS output -options. -

    -

    All array values calculated by this compute are "intensive". -

    -

    Restrictions: -

    -

    The compute_xrd command does not work for triclinic cells. -

    -

    Related commands: -

    -

    fix ave/histo, -compute saed -

    -

    Default: -

    -

    The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, -no manual flag, no echo flag. -

    -
    - - - -

    (Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 -(2013). -

    - - -

    (Colliex) Colliex et al. International Tables for Crystallography -Volume C: Mathematical and Chemical Tables, 249-429 (2004). -

    - - -

    (Peng) Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 -(1996). -

    - diff --git a/doc/doc2/create_atoms.html b/doc/doc2/create_atoms.html deleted file mode 100644 index dff7b6c971..0000000000 --- a/doc/doc2/create_atoms.html +++ /dev/null @@ -1,329 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    create_atoms command -

    -

    Syntax: -

    -
    create_atoms type style args keyword values ... 
-
    -
    • type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) - -
    • style = box or region or single or random - -
        box args = none
-  region args = region-ID
-    region-ID = particles will only be created if contained in the region
-  single args = x y z
-    x,y,z = coordinates of a single particle (distance units)
-  random args = N seed region-ID
-    N = number of particles to create
-    seed = random # seed (positive integer)
-    region-ID = create atoms within this region, use NULL for entire simulation box 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = mol or basis or remap or var or set or units - -
        mol value = template-ID seed
-    template-ID = ID of molecule template specified in a separate molecule command
-    seed = random # seed (positive integer)
-  basis values = M itype
-    M = which basis atom
-    itype = atom type (1-N) to assign to this basis atom
-  remap value = yes or no
-  var value = name = variable name to evaluate for test of atom creation
-  set values = dim vname
-    dim = x or y or z
-    name = name of variable to set with x,y,z atom position
-  rotate values = Rx Ry Rz theta
-    Rx,Ry,Rz = rotation vector for single molecule
-    theta = rotation angle for single molecule (degrees)
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    create_atoms 1 box
-create_atoms 3 region regsphere basis 2 3
-create_atoms 3 single 0 0 5 
-create_atoms 1 box var v set x xpos set y ypos 
-
    -

    Description: -

    -

    This command creates atoms (or molecules) on a lattice, or a single -atom (or molecule), or a random collection of atoms (or molecules), as -an alternative to reading in their coordinates explicitly via a -read_data or read_restart -command. A simulation box must already exist, which is typically -created via the create_box command. Before using -this command, a lattice must also be defined using the -lattice command, unless you specify the single style -with units = box or the random style. For the remainder of this doc -page, a created atom or molecule is referred to as a "particle". -

    -

    If created particles are individual atoms, they are assigned the -specified atom type, though this can be altered via the basis -keyword as discussed below. If molecules are being created, the type -of each atom in the created molecule is specified in the file read by -the molecule command, and those values are added to -the specified atom type. E.g. if type = 2, and the file specifies -atom types 1,2,3, then each created molecule will have atom types -3,4,5. -

    -

    For the box style, the create_atoms command fills the entire -simulation box with particles on the lattice. If your simulation box -is periodic, you should insure its size is a multiple of the lattice -spacings, to avoid unwanted atom overlaps at the box boundaries. If -your box is periodic and a multiple of the lattice spacing in a -particular dimension, LAMMPS is careful to put exactly one particle at -the boundary (on either side of the box), not zero or two. -

    -

    For the region style, a geometric volume is filled with particles on -the lattice. This volume what is inside the simulation box and is -also consistent with the region volume. See the region -command for details. Note that a region can be specified so that its -"volume" is either inside or outside a geometric boundary. Also note -that if your region is the same size as a periodic simulation box (in -some dimension), LAMMPS does not implement the same logic described -above as for the box style, to insure exactly one particle at -periodic boundaries. if this is what you desire, you should either -use the box style, or tweak the region size to get precisely the -particles you want. -

    -

    For the single style, a single particle is added to the system at -the specified coordinates. This can be useful for debugging purposes -or to create a tiny system with a handful of particles at specified -positions. -

    -

    For the random style, N particles are added to the system at -randomly generated coordinates, which can be useful for generating an -amorphous system. The particles are created one by one using the -speficied random number seed, resulting in the same set of particles -coordinates, independent of how many processors are being used in the -simulation. If the region-ID argument is specified as NULL, then -the created particles will be anywhere in the simulation box. If a -region-ID is specified, a geometric volume is filled which is both -inside the simulation box and is also consistent with the region -volume. See the region command for details. Note that -a region can be specified so that its "volume" is either inside or -outside a geometric boundary. -

    -

    IMPORTANT NOTE: Particles generated by the random style will -typically be highly overlapped which will cause many interatomic -potentials to compute large energies and forces. Thus you should -either perform an energy minimization or run dynamics -with fix nve/limit to equilibrate such a system, -before running normal dynamics. -

    -

    Note that this command adds particles to those that already exist. -This means it can be used to add particles to a system previously read -in from a data or restart file. Or the create_atoms command can be -used multiple times, to add multiple sets of particles to the -simulation. For example, grain boundaries can be created, by -interleaving create_atoms with lattice commands -specifying different orientations. By using the create_atoms command -in conjunction with the delete_atoms command, -reasonably complex geometries can be created, or a protein can be -solvated with a surrounding box of water molecules. -

    -

    In all these cases, care should be taken to insure that new atoms do -not overlap existing atoms inappropriately, especially if molecules -are being added. The delete_atoms command can be -used to remove overlapping atoms or molecules. -

    -
    - -

    Individual atoms are inserted by this command, unless the mol -keyword is used. It specifies a template-ID previously defined -using the molecule command, which reads a file that -defines the molecule. The coordinates, atom types, charges, etc, as -well as any bond/angle/etc and special neighbor information for the -molecule can be specified in the molecule file. See the -molecule command for details. The only settings -required to be in this file are the coordinates and types of atoms in -the molecule. -

    -

    Using a lattice to add molecules, e.g. via the box or region or -single styles, is exactly the same as adding atoms on lattice -points, except that entire molecules are added at each point, i.e. on -the point defined by each basis atom in the unit cell as it tiles the -simulation box or region. This is done by placing the geometric -center of the molecule at the lattice point, and giving the molecule a -random orientation about the point. The random seed specified with -the mol keyword is used for this operation, and the random numbers -generated by each processor are different. This means the coordinates -of individual atoms (in the molecules) will be different when running -on different numbers of processors, unlike when atoms are being -created in parallel. -

    -

    Also note that because of the random rotations, it may be important to -use a lattice with a large enough spacing that adjacent molecules will -not overlap, regardless of their relative orientations. -

    -

    IMPORTANT NOTE: If the create_box command is used to -create the simulation box, followed by the create_atoms command with -its mol option for adding molecules, then you typically need to use -the optional keywords allowed by the create_box -command for extra bonds (angles,etc) or extra special neighbors. This -is because by default, the create_box command sets -up a non-molecular system which doesn't allow molecules to be added. -

    -
    - -

    This is the meaning of the other allowed keywords. -

    -

    The basis keyword is only used when atoms (not molecules) are being -created. It specifies an atom type that will be assigned to specific -basis atoms as they are created. See the lattice -command for specifics on how basis atoms are defined for the unit cell -of the lattice. By default, all created atoms are assigned the -argument type as their atom type. -

    -

    The remap keyword only applies to the single style. If it is set -to yes, then if the specified position is outside the simulation -box, it will mapped back into the box, assuming the relevant -dimensions are periodic. If it is set to no, no remapping is done -and no particle is created if its position is outside the box. -

    -

    The var and set keywords can be used to provide a criterion for -accepting or rejecting the addition of an individual atom, based on -its coordinates. The vname specified for the var keyword is the -name of an equal-style variable which should evaluate -to a zero or non-zero value based on one or two or three variables -which will store the x, y, or z coordinates of an atom (one variable -per coordinate). These other variables must be equal-style -variables defined in the input script, but their -formula can by anything. The set keyword is used to identify the -names of these other variables, one variable for the x-coordinate of a -created atom, one for y, and one for z. -

    -

    When an atom is created, its x, y, or z coordinates override the -formula for any set variable that is defined. The var variable is -then evaluated. If the returned value is 0.0, the atom is not -created. If it is non-zero, the atom is created. After all atoms are -created, the formulas defined for all of the set variables are -restored to their original strings. -

    -

    As an example, these commands can be used in a 2d simulation, to -create a sinusoidal surface. Note that the surface is "rough" due to -individual lattice points being "above" or "below" the mathematical -expression for the sinusoidal curve. If a finer lattice were used, -the sinusoid would appear to be "smoother". Also note the use of the -"xlat" and "ylat" thermo_style keywords which -converts lattice spacings to distance. Click on the image for a -larger version. -

    -
    variable        x equal 100
-variable        y equal 25
-lattice		hex 0.8442
-region		box block 0 $x 0 $y -0.5 0.5
-create_box	1 box 
-
    -
    variable        xx equal 0.0
-variable        yy equal 0.0
-variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-create_atoms	1 box var v set x xx set y yy 
-
    -
    -
    -

    The rotate keyword can be used with the single style, when adding -a single molecule to specify the orientation at which the molecule is -inserted. The axis of rotation is determined by the rotation vector -(Rx,Ry,Rz) that goes through the insertion point. The specified -theta determines the angle of rotation around that axis. Note that -the direction of rotation for the atoms around the rotation axis is -consistent with the right-hand rule: if your right-hand's thumb points -along R, then your fingers wrap around the axis in the direction of -rotation. -

    -

    The units keyword determines the meaning of the distance units used -to specify the coordinates of the one particle created by the single -style. A box value selects standard distance units as defined by -the units command, e.g. Angstroms for units = real or -metal. A lattice value means the distance units are in lattice -spacings. -

    -
    - -

    Atom IDs are assigned to created atoms in the following way. The -collection of created atoms are assigned consecutive IDs that start -immediately following the largest atom ID existing before the -create_atoms command was invoked. When a simulation is performed on -different numbers of processors, there is no guarantee a particular -created atom will be assigned the same ID. If molecules are being -created, molecule IDs are assigned to created molecules in a similar -fashion. -

    -

    Aside from their ID, atom type, and xyz position, other properties of -created atoms are set to default values, depending on which quantities -are defined by the chosen atom style. See the atom -style command for more details. See the -set and velocity commands for info on how -to change these values. -

    -
    • charge = 0.0 -
    • dipole moment magnitude = 0.0 -
    • diameter = 1.0 -
    • shape = 0.0 0.0 0.0 -
    • density = 1.0 -
    • volume = 1.0 -
    • velocity = 0.0 0.0 0.0 -
    • angular velocity = 0.0 0.0 0.0 -
    • angular momentum = 0.0 0.0 0.0 -
    • quaternion = (1,0,0,0) -
    • bonds, angles, dihedrals, impropers = none -
    -

    If molecules are being created, these defaults can be overridden by -values specified in the file read by the molecule -command. E.g. the file typically defines bonds (angles,etc) between -atoms in the molecule, and can optionally define charges on each atom. -

    -

    Note that the sphere atom style sets the default particle diameter -to 1.0 as well as the density. This means the mass for the particle -is not 1.0, but is PI/6 * diameter^3 = 0.5236. -

    -

    Note that the ellipsoid atom style sets the default particle shape -to (0.0 0.0 0.0) and the density to 1.0 which means it is a point -particle, not an ellipsoid, and has a mass of 1.0. -

    -

    Note that the peri style sets the default volume and density to 1.0 -and thus also set the mass for the particle to 1.0. -

    -

    The set command can be used to override many of these -default settings. -

    -
    - -

    Restrictions: -

    -

    An atom_style must be previously defined to use this -command. -

    -

    A rotation vector specified for a single molecule must be in -the z-direction for a 2d model. -

    -

    Related commands: -

    -

    lattice, region, create_box, -read_data, read_restart -

    -

    Default: -

    -

    The default for the basis keyword is that all created atoms are -assigned the argument type as their atom type (when single atoms are -being created). The other defaults are remap = no, rotate = -random, and units = lattice. -

    - diff --git a/doc/doc2/create_bonds.html b/doc/doc2/create_bonds.html deleted file mode 100644 index 13267df97f..0000000000 --- a/doc/doc2/create_bonds.html +++ /dev/null @@ -1,114 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    create_bonds command -

    -

    Syntax: -

    -
    create_bonds group-ID group2-ID btype rmin rmax 
-
    -
    • group-ID = ID of first group -
    • group2-ID = ID of second group, bonds will be between atoms in the 2 groups -
    • btype = bond type of created bonds -
    • rmin = minimum distance between pair of atoms to bond together -
    • rmax = minimum distance between pair of atoms to bond together -
    -

    Examples: -

    -
    create_bonds all all 1 1.0 1.2
-create_bonds surf solvent 3 2.0 2.4 
-
    -

    Description: -

    -

    Create bonds between pairs of atoms that meet specified distance -criteria. The bond interactions can then be computed during a -simulation by the bond potential defined by the -bond_style and bond_coeff -commands. This command is useful for adding bonds to a system, -e.g. between nearest neighbors in a lattice of atoms, without having -to enumerate all the bonds in the data file read by the -read_data command. -

    -

    Note that the flexibility of this command is limited. It can be used -several times to create different types of bond at different -distances. But it cannot typically create all the bonds that would -normally be defined in a complex system of molecules. Also note that -this command does not add any 3-body or 4-body interactions which, -depending on your model, may be induced by added bonds, -e.g. angle, dihedral, or -improper interactions. -

    -

    All created bonds will be between pairs of atoms I,J where I is in one -of the two specified groups, and J is in the other. The two groups -can be the same, e.g. group "all". The created bonds will be of bond -type btype, where btype must be a value between 1 and the number -of bond types defined. This maximum value is set by the "bond types" -field in the header of the data file read by the -read_data command, or via the optional "bond/types" -argument of the create_box command. -

    -

    For a bond to be created, an I,J pair of atoms must be a distance D -apart such that rmin <= D <= rmax. -

    -

    The following settings must have been made in an input -script before this command is used: -

    - -

    These settings are required so that a neighbor list can be created to -search for nearby atoms. Pairs of atoms that are already bonded -cannot appear in the neighbor list, to avoid creation of duplicate -bonds. The neighbor list for all atom type pairs must also extend to -a distance that encompasses the rmax for new bonds to create. -

    -

    An additional requirement is that your system must be ready to perform -a simulation. This means, for example, that all -pair_style coefficients be set via the -pair_coeff command. A bond_style -command and all bond coefficients must also be set, even if no bonds -exist before this command is invoked. This is because the building of -neighbor list requires initialization and setup of a simulation, -similar to what a run command would require. -

    -

    Note that you can change any of these settings after this command -executes, e.g. if you wish to use long-range Coulombic interactions -via the kspace_style command for your subsequent -simulation. -

    -

    IMPORTANT NOTE: If the system has no bonds to begin with, or if more -bonds per atom are being added than currently exist, then you must -insure that the number of bond types and the maximum number of bonds -per atom are set to large enough values. Otherwise an error may occur -when too many bonds are added to an atom. If the -read_data command is used to define the system, these -2 parameters can be set via the "bond types" and "extra bond per atom" -fields in the header section of the data file. If the -create_box command is used to define the system, -these 2 parameters can be set via its optional "bond/types" and -"extra/bond/per/atom" arguments. See the doc pages for the 2 commands -for details. -

    -

    Restrictions: -

    -

    This command cannot be used with molecular systems defined using -molecule template files via the molecule and -atom_style template commands. -

    -

    Related commands: -

    -

    create_atoms, delete_bonds -

    -

    Default: none -

    - diff --git a/doc/doc2/create_box.html b/doc/doc2/create_box.html deleted file mode 100644 index 85be5f5f61..0000000000 --- a/doc/doc2/create_box.html +++ /dev/null @@ -1,162 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    create_box command -

    -

    Syntax: -

    -
    create_box N region-ID keyword value ... 
-
    -
    • N = # of atom types to use in this simulation - -
    • region-ID = ID of region to use as simulation domain - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = bond/types or angle/types or dihedral/types or improper/types or extra/bond/per/atom or extra/angle/per/atom or extra/dihedral/per/atom or extra/improper/per/atom - -
        bond/types value = # of bond types
-  angle/types value = # of angle types
-  dihedral/types value = # of dihedral types
-  improper/types value = # of improper types
-  extra/bond/per/atom value = # of bonds per atom
-  extra/angle/per/atom value = # of angles per atom
-  extra/dihedral/per/atom value = # of dihedrals per atom
-  extra/improper/per/atom value = # of impropers per atom
-  extra/special/per/atom value = # of special neighbors per atom 
-
      - -
    -

    Examples: -

    -
    create_box 2 mybox
-create_box 2 mybox bond/types 2 extra/bond/per/atom 1 
-
    -

    Description: -

    -

    This command creates a simulation box based on the specified region. -Thus a region command must first be used to define a -geometric domain. It also partitions the simulation box into a -regular 3d grid of rectangular bricks, one per processor, based on the -number of processors being used and the settings of the -processors command. The partitioning can later be -changed by the balance or fix -balance commands. -

    -

    The argument N is the number of atom types that will be used in the -simulation. -

    -

    If the region is not of style prism, then LAMMPS encloses the region -(block, sphere, etc) with an axis-aligned orthogonal bounding box -which becomes the simulation domain. -

    -

    If the region is of style prism, LAMMPS creates a non-orthogonal -simulation domain shaped as a parallelepiped with triclinic symmetry. -As defined by the region prism command, the -parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3 -edge vectors starting from the origin given by A = (xhi-xlo,0,0); B = -(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). Xy,xz,yz can be 0.0 or -positive or negative values and are called "tilt factors" because they -are the amount of displacement applied to faces of an originally -orthogonal box to transform it into the parallelipiped. -

    -

    By default, a prism region used with the create_box command must -have tilt factors (xy,xz,yz) that do not skew the box more than half -the distance of the parallel box length. For example, if xlo = 2 and -xhi = 12, then the x box length is 10 and the xy tilt factor must be -between -5 and 5. Similarly, both xz and yz must be between --(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, -since if the maximum tilt factor is 5 (as in this example), then -configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all -geometrically equivalent. If you wish to define a box with tilt -factors that exceed these limits, you can use the box tilt -command, with a setting of large; a setting of small is the -default. -

    -

    See Section_howto 12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used -triclinic representations. -

    -

    When a prism region is used, the simulation domain should normally be -periodic in the dimension that the tilt is applied to, which is given -by the second dimension of the tilt factor (e.g. y for xy tilt). This -is so that pairs of atoms interacting across that boundary will have -one of them shifted by the tilt factor. Periodicity is set by the -boundary command. For example, if the xy tilt factor -is non-zero, then the y dimension should be periodic. Similarly, the -z dimension should be periodic if xz or yz is non-zero. LAMMPS does -not require this periodicity, but you may lose atoms if this is not -the case. -

    -

    Also note that if your simulation will tilt the box, e.g. via the fix -deform command, the simulation box must be setup to -be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by -using the change box command with its ortho and -triclinic options. -

    -

    IMPORTANT NOTE: If the system is non-periodic (in a dimension), then -you should not make the lo/hi box dimensions (as defined in your -region command) radically smaller/larger than the extent -of the atoms you eventually plan to create, e.g. via the -create_atoms command. For example, if your atoms -extend from 0 to 50, you should not specify the box bounds as -10000 -and 10000. This is because as described above, LAMMPS uses the -specified box size to layout the 3d grid of processors. A huge -(mostly empty) box will be sub-optimal for performance when using -"fixed" boundary conditions (see the boundary -command). When using "shrink-wrap" boundary conditions (see the -boundary command), a huge (mostly empty) box may cause -a parallel simulation to lose atoms the first time that LAMMPS -shrink-wraps the box around the atoms. -

    -
    - -

    The optional keywords can be used to create a system that allows for -bond (angle, dihedral, improper) interactions, or for molecules with -special 1-2,1-3,1-4 neighbors to be added later. These optional -keywords serve the same purpose as the analogous keywords that can be -used in a data file which are recognized by the -read_data command when it sets up a system. -

    -

    Note that if these keywords are not used, then the create_box command -creates an atomic (non-molecular) simulation that does not allow bonds -between pairs of atoms to be defined, or a bond -potential to be specified, or for molecules with -special neighbors to be added to the system by commands such as -create_atoms mol, fix deposit -or fix pour. -

    -

    As an example, see the examples/deposit/in.deposit.molecule script, -which deposits molecules onto a substrate. Initially there are no -molecules in the system, but they are added later by the fix -deposit command. The create_box command in the -script uses the bond/types and extra/bond/per/atom keywords to allow -this. If the added molecule contained more than 1 special bond -(allowed by default), an extra/special/per/atom keyword would also -need to be specified. -

    -
    - -

    Restrictions: -

    -

    An atom_style and region must have -been previously defined to use this command. -

    -

    Related commands: -

    -

    read_data, create_atoms, -region -

    -

    Default: none -

    - diff --git a/doc/doc2/delete_atoms.html b/doc/doc2/delete_atoms.html deleted file mode 100644 index 9e2a0eadb1..0000000000 --- a/doc/doc2/delete_atoms.html +++ /dev/null @@ -1,154 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    delete_atoms command -

    -

    Syntax: -

    -
    delete_atoms style args keyword value ... 
-
    -
    • style = group or region or overlap or porosity - -
        group args = group-ID
-  region args = region-ID
-  overlap args = cutoff group1-ID group2-ID
-    cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
-    group1-ID = one atom in pair must be in this group
-    group2-ID = other atom in pair must be in this group
-  porosity args = region-ID fraction seed
-    region-ID = region within which to perform deletions
-    fraction = delete this fraction of atoms
-    seed = random number seed (positive integer) 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = compress or bond or mol - -
        compress value = no or yes
-  bond value = no or yes
-  mol value = no or yes 
-
      - -
    -

    Examples: -

    -
    delete_atoms group edge
-delete_atoms region sphere compress no
-delete_atoms overlap 0.3 all all
-delete_atoms overlap 0.5 solvent colloid
-delete_atoms porosity cube 0.1 482793 bond yes 
-
    -

    Description: -

    -

    Delete the specified atoms. This command can be used to carve out -voids from a block of material or to delete created atoms that are too -close to each other (e.g. at a grain boundary). -

    -

    For style group, all atoms belonging to the group are deleted. -

    -

    For style region, all atoms in the region volume are deleted. -Additional atoms can be deleted if they are in a molecule for which -one or more atoms were deleted within the region; see the mol -keyword discussion below. -

    -

    For style overlap pairs of atoms whose distance of separation is -within the specified cutoff distance are searched for, and one of the -2 atoms is deleted. Only pairs where one of the two atoms is in the -first group specified and the other atom is in the second group are -considered. The atom that is in the first group is the one that is -deleted. -

    -

    Note that it is OK for the two group IDs to be the same (e.g. group -all), or for some atoms to be members of both groups. In these -cases, either atom in the pair may be deleted. Also note that if -there are atoms which are members of both groups, the only guarantee -is that at the end of the deletion operation, enough deletions will -have occurred that no atom pairs within the cutoff will remain -(subject to the group restriction). There is no guarantee that the -minimum number of atoms will be deleted, or that the same atoms will -be deleted when running on different numbers of processors. -

    -

    For style porosity a specified fraction of atoms are deleted -within the specified region. For example, if fraction is 0.1, then -10% of the atoms will be deleted. The atoms to delete are chosen -randomly. There is no guarantee that the exact fraction of atoms will -be deleted, or that the same atoms will be deleted when running on -different numbers of processors. -

    -

    If the compress keyword is set to yes, then after atoms are -deleted, then atom IDs are re-assigned so that they run from 1 to the -number of atoms in the system. Note that this is not done for -molecular systems (see the atom_style command), -regardless of the compress setting, since it would foul up the bond -connectivity that has already been assigned. -

    -

    A molecular system with fixed bonds, angles, dihedrals, or improper -interactions, is one where the topology of the interactions is -typically defined in the data file read by the -read_data command, and where the interactions -themselves are defined with the bond_style, -angle_style, etc commands. If you delete atoms -from such a system, you must be careful not to end up with bonded -interactions that are stored by remaining atoms but which include -deleted atoms. This will cause LAMMPS to generate a "missing atoms" -error when the bonded interaction is computed. The bond and mol -keywords offer two ways to do that. -

    -

    It the bond keyword is set to yes then any bond or angle or -dihedral or improper interaction that includes a deleted atom is also -removed from the lists of such interactions stored by non-deleted -atoms. Note that simply deleting interactions due to dangling bonds -(e.g. at a surface) may result in a inaccurate or invalid model for -the remaining atoms. -

    -

    It the mol keyword is set to yes, then for every atom that is -deleted, all other atoms in the same molecule (with the same molecule -ID) will also be deleted. This is not done for atoms with molecule ID -= 0, since such an ID is assumed to flag isolated atoms that are not -part of molecules. -

    -

    IMPORTANT NOTE: The molecule deletion operation in invoked after all -individual atoms have been deleted using the rules described above for -each style. This means additional atoms may be deleted that are not -in the group or region, that are not required by the overlap cutoff -criterion, or that will create a higher fraction of porosity than was -requested. -

    -

    Restrictions: -

    -

    The overlap styles requires inter-processor communication to acquire -ghost atoms and build a neighbor list. This means that your system -must be ready to perform a simulation before using this command (force -fields setup, atom masses set, etc). Since a neighbor list is used to -find overlapping atom pairs, it also means that you must define a -pair style with the minimum force cutoff distance -between any pair of atoms types (plus the neighbor -skin) >= the specified overlap cutoff. -

    -

    If the special_bonds command is used with a -setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not -appear in the neighbor list, and thus will not be considered for -deletion by the overlap styles. You probably don't want to be -deleting one atom in a bonded pair anyway. -

    -

    The bond yes option cannot be used with molecular systems defined -using molecule template files via the molecule and -atom_style template commands. -

    -

    Related commands: -

    -

    create_atoms -

    -

    Default: -

    -

    The option defaults are compress = yes, bond = no, mol = no. -

    - diff --git a/doc/doc2/delete_bonds.html b/doc/doc2/delete_bonds.html deleted file mode 100644 index ccd35f4526..0000000000 --- a/doc/doc2/delete_bonds.html +++ /dev/null @@ -1,159 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    delete_bonds command -

    -

    Syntax: -

    -
    delete_bonds group-ID style arg keyword ... 
-
    -
    • group-ID = group ID - -
    • style = multi or atom or bond or angle or dihedral or - improper or stats - -
        multi arg = none
-  atom arg = an atom type or range of types (see below)
-  bond arg = a bond type or range of types (see below)
-  angle arg = an angle type or range of types (see below)
-  dihedral arg = a dihedral type or range of types (see below)
-  improper arg = an improper type or range of types (see below)
-  stats arg = none 
-
      -
    • zero or more keywords may be appended - -
    • keyword = any or undo or remove or special - - -
    -

    Examples: -

    -
    delete_bonds frozen multi remove
-delete_bonds all atom 4 special
-delete_bonds all bond 0*3 special
-delete_bonds all stats 
-
    -

    Description: -

    -

    Turn off (or on) molecular topology interactions, i.e. bonds, angles, -dihedrals, impropers. This command is useful for deleting -interactions that have been previously turned off by bond-breaking -potentials. It is also useful for turning off topology interactions -between frozen or rigid atoms. Pairwise interactions can be turned -off via the neigh_modify exclude command. The -fix shake command also effectively turns off certain -bond and angle interactions. -

    -

    For all styles, by default, an interaction is only turned off (or on) -if all the atoms involved are in the specified group. See the any -keyword to change the behavior. -

    -

    Several of the styles (atom, bond, angle, dihedral, -improper) take a type as an argument. The specified type should -be an integer from 0 to N, where N is the number of relevant types -(atom types, bond types, etc). A value of 0 is only relevant for -style bond; see details below. In all cases, a wildcard asterisk -can be used in place of or in conjunction with the type argument to -specify a range of types. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the number of types, then an asterisk with no numeric -values means all types from 0 to N. A leading asterisk means all -types from 0 to n (inclusive). A trailing asterisk means all types -from n to N (inclusive). A middle asterisk means all types from m to -n (inclusive). Note that it is fine to include a type of 0 for -non-bond styles; it will simply be ignored. -

    -

    For style multi all bond, angle, dihedral, and improper interactions -of any type, involving atoms in the group, are turned off. -

    -

    Style atom is the same as style multi except that in addition, one -or more of the atoms involved in the bond, angle, dihedral, or -improper interaction must also be of the specified atom type. -

    -

    For style bond, only bonds are candidates for turn-off, and the bond -must also be of the specified type. Styles angle, dihedral, and -improper are treated similarly. -

    -

    For style bond, you can set the type to 0 to delete bonds that have -been previously broken by a bond-breaking potential (which sets the -bond type to 0 when a bond is broken); e.g. see the bond_style -quartic command. -

    -

    For style stats no interactions are turned off (or on); the status -of all interactions in the specified group is simply reported. This -is useful for diagnostic purposes if bonds have been turned off by a -bond-breaking potential during a previous run. -

    -

    The default behavior of the delete_bonds command is to turn off -interactions by toggling their type to a negative value, but not to -permanently remove the interaction. E.g. a bond_type of 2 is set to --2. The neighbor list creation routines will not include such an -interaction in their interaction lists. The default is also to not -alter the list of 1-2, 1-3, 1-4 neighbors computed by the -special_bonds command and used to weight pairwise -force and energy calculations. This means that pairwise computations -will proceed as if the bond (or angle, etc) were still turned on. -

    -

    Several keywords can be appended to the argument list to alter the -default behaviors. -

    -

    The any keyword changes the requirement that all atoms in the bond -(angle, etc) must be in the specified group in order to turn-off the -interaction. Instead, if any of the atoms in the interaction are in -the specified group, it will be turned off (or on if the undo -keyword is used). -

    -

    The undo keyword inverts the delete_bonds command so that the -specified bonds, angles, etc are turned on if they are currently -turned off. This means a negative value is toggled to positive. For -example, for style angle, if type is specified as 2, then all -angles with current type = -2, are reset to type = 2. Note that the -fix shake command also sets bond and angle types -negative, so this option should not be used on those interactions. -

    -

    The remove keyword is invoked at the end of the delete_bonds -operation. It causes turned-off bonds (angles, etc) to be removed -from each atom's data structure and then adjusts the global bond -(angle, etc) counts accordingly. Removal is a permanent change; -removed bonds cannot be turned back on via the undo keyword. -Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list. -

    -

    The special keyword is invoked at the end of the delete_bonds -operation, after (optional) removal. It re-computes the pairwise 1-2, -1-3, 1-4 weighting list. The weighting list computation treats -turned-off bonds the same as turned-on. Thus, turned-off bonds must -be removed if you wish to change the weighting list. -

    -

    Note that the choice of remove and special options affects how -1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that -have been modified by the delete_bonds command. -

    -

    Restrictions: -

    -

    This command requires inter-processor communication to coordinate the -deleting of bonds. This means that your system must be ready to -perform a simulation before using this command (force fields setup, -atom masses set, etc). -

    -

    If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4 -weighting list is not recomputed, this can cause a later fix -shake command to fail due to an atom's bonds being -inconsistent with the weighting list. This should only happen if the -group used in the fix command includes both atoms in the bond, in -which case you probably should be recomputing the weighting list. -

    -

    Related commands: -

    -

    neigh_modify exclude, -special_bonds, fix shake -

    -

    Default: none -

    - diff --git a/doc/doc2/dielectric.html b/doc/doc2/dielectric.html deleted file mode 100644 index 9ba1459bcd..0000000000 --- a/doc/doc2/dielectric.html +++ /dev/null @@ -1,44 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dielectric command -

    -

    Syntax: -

    -
    dielectric value 
-
    -
    • value = dielectric constant -
    -

    Examples: -

    -
    dielectric 2.0 
-
    -

    Description: -

    -

    Set the dielectric constant for Coulombic interactions (pairwise and -long-range) to this value. The constant is unitless, since it is used -to reduce the strength of the interactions. The value is used in the -denominator of the formulas for Coulombic interactions - e.g. a value -of 4.0 reduces the Coulombic interactions to 25% of their default -strength. See the pair_style command for more -details. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_style -

    -

    Default: -

    -
    dielectric 1.0 
-
    - diff --git a/doc/doc2/dihedral_charmm.html b/doc/doc2/dihedral_charmm.html deleted file mode 100644 index 10a1588f63..0000000000 --- a/doc/doc2/dihedral_charmm.html +++ /dev/null @@ -1,123 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style charmm command -

    -

    dihedral_style charmm/kk command -

    -

    dihedral_style charmm/omp command -

    -

    Syntax: -

    -
    dihedral_style charmm 
-
    -

    Examples: -

    -
    dihedral_style charmm
-dihedral_coeff 1 120.0 1 60 0.5 
-
    -

    Description: -

    -

    The charmm dihedral style uses the potential -

    -
    -
    -

    See (MacKerell) for a description of the CHARMM force -field. This dihedral style can also be used for the AMBER force field -(see comment on weighting factors below). See (Cornell) -for a description of the AMBER force field. -

    -

    The following coefficients must be defined for each dihedral type via the -dihedral_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    • n (integer >= 0) -
    • d (integer value of degrees) -
    • weighting factor (0.0 to 1.0) -
    -

    The weighting factor is applied to pairwise interaction between the -1st and 4th atoms in the dihedral, which are computed by a CHARMM -pair_style with epsilon and sigma values specified -with a pair_coeff command. Note that this -weighting factor is unrelated to the weighting factor specified by the -special bonds command which applies to all 1-4 -interactions in the system. -

    -

    For CHARMM force fields, the special_bonds 1-4 weighting factor should -be set to 0.0. This is because the pair styles that contain "charmm" -(e.g. pair_style lj/charmm/coul/long) define extra -1-4 interaction coefficients that are used by this dihedral style to -compute those interactions explicitly. This means that if any of the -weighting factors defined as dihedral coefficients (4th coeff above) -are non-zero, then you must use a charmm pair style. Note that if you -do not set the special_bonds 1-4 weighting factor to 0.0 (which is the -default) then 1-4 interactions in dihedrals will be computed twice, -once by the pair routine and once by the dihedral routine, which is -probably not what you want. -

    -

    For AMBER force fields, the special_bonds 1-4 weighting factor should -be set to the AMBER defaults (1/2 and 5/6) and all the dihedral -weighting factors (4th coeff above) should be set to 0.0. In this -case, you can use any pair style you wish, since the dihedral does not -need any 1-4 information. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    -
    - - - -

    (Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). -

    - - -

    (MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998). -

    - diff --git a/doc/doc2/dihedral_class2.html b/doc/doc2/dihedral_class2.html deleted file mode 100644 index 1dc4af3f4e..0000000000 --- a/doc/doc2/dihedral_class2.html +++ /dev/null @@ -1,185 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style class2 command -

    -

    dihedral_style class2/omp command -

    -

    Syntax: -

    -
    dihedral_style class2 
-
    -

    Examples: -

    -
    dihedral_style class2
-dihedral_coeff 1 100 75 100 70 80 60
-dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 
-dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
-dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 
-dihedral_coeff * aat -13.5271 110.2453 105.1270 
-dihedral_coeff * bb13 0.0 1.0119 1.1010 
-
    -

    Description: -

    -

    The class2 dihedral style uses the potential -

    -
    -
    -

    where Ed is the dihedral term, Embt is a middle-bond-torsion term, -Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat -is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term. -

    -

    Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium -bond lengths. -

    -

    See (Sun) for a description of the COMPASS class2 force field. -

    -

    Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas -must be defined for each dihedral type via the -dihedral_coeff command as in the example above, -or in the data file or restart files read by the -read_data or read_restart -commands. -

    -

    These are the 6 coefficients for the Ed formula: -

    -
    • K1 (energy) -
    • phi1 (degrees) -
    • K2 (energy) -
    • phi2 (degrees) -
    • K3 (energy) -
    • phi3 (degrees) -
    -

    For the Embt formula, each line in a -dihedral_coeff command in the input script lists -5 coefficients, the first of which is "mbt" to indicate they are -MiddleBondTorsion coefficients. In a data file, these coefficients -should be listed under a "MiddleBondTorsion Coeffs" heading and you -must leave out the "mbt", i.e. only list 4 coefficients after the -dihedral type. -

    -
    • mbt -
    • A1 (energy/distance) -
    • A2 (energy/distance) -
    • A3 (energy/distance) -
    • r2 (distance) -
    -

    For the Eebt formula, each line in a -dihedral_coeff command in the input script lists -9 coefficients, the first of which is "ebt" to indicate they are -EndBondTorsion coefficients. In a data file, these coefficients -should be listed under a "EndBondTorsion Coeffs" heading and you must -leave out the "ebt", i.e. only list 8 coefficients after the dihedral -type. -

    -
    • ebt -
    • B1 (energy/distance) -
    • B2 (energy/distance) -
    • B3 (energy/distance) -
    • C1 (energy/distance) -
    • C2 (energy/distance) -
    • C3 (energy/distance) -
    • r1 (distance) -
    • r3 (distance) -
    -

    For the Eat formula, each line in a -dihedral_coeff command in the input script lists -9 coefficients, the first of which is "at" to indicate they are -AngleTorsion coefficients. In a data file, these coefficients should -be listed under a "AngleTorsion Coeffs" heading and you must leave out -the "at", i.e. only list 8 coefficients after the dihedral type. -

    -
    • at -
    • D1 (energy/radian) -
    • D2 (energy/radian) -
    • D3 (energy/radian) -
    • E1 (energy/radian) -
    • E2 (energy/radian) -
    • E3 (energy/radian) -
    • theta1 (degrees) -
    • theta2 (degrees) -
    -

    Theta1 and theta2 are specified in degrees, but LAMMPS converts them -to radians internally; hence the units of D and E are in -energy/radian. -

    -

    For the Eaat formula, each line in a -dihedral_coeff command in the input script lists -4 coefficients, the first of which is "aat" to indicate they are -AngleAngleTorsion coefficients. In a data file, these coefficients -should be listed under a "AngleAngleTorsion Coeffs" heading and you -must leave out the "aat", i.e. only list 3 coefficients after the -dihedral type. -

    -
    • aat -
    • M (energy/radian^2) -
    • theta1 (degrees) -
    • theta2 (degrees) -
    -

    Theta1 and theta2 are specified in degrees, but LAMMPS converts them -to radians internally; hence the units of M are in energy/radian^2. -

    -

    For the Ebb13 formula, each line in a -dihedral_coeff command in the input script lists -4 coefficients, the first of which is "bb13" to indicate they are -BondBond13 coefficients. In a data file, these coefficients should be -listed under a "BondBond13 Coeffs" heading and you must leave out the -"bb13", i.e. only list 3 coefficients after the dihedral type. -

    -
    • bb13 -
    • N (energy/distance^2) -
    • r1 (distance) -
    • r3 (distance) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -CLASS2 package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    -
    - - - -

    (Sun) Sun, J Phys Chem B 102, 7338-7364 (1998). -

    - diff --git a/doc/doc2/dihedral_coeff.html b/doc/doc2/dihedral_coeff.html deleted file mode 100644 index 5461b7e706..0000000000 --- a/doc/doc2/dihedral_coeff.html +++ /dev/null @@ -1,113 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_coeff command -

    -

    Syntax: -

    -
    dihedral_coeff N args 
-
    -
    • N = dihedral type (see asterisk form below) -
    • args = coefficients for one or more dihedral types -
    -

    Examples: -

    -
    dihedral_coeff 1 80.0 1 3
-dihedral_coeff * 80.0 1 3 0.5
-dihedral_coeff 2* 80.0 1 3 0.5 
-
    -

    Description: -

    -
    - -

    Specify the dihedral force field coefficients for one or more dihedral types. -The number and meaning of the coefficients depends on the dihedral style. -Dihedral coefficients can also be set in the data file read by the -read_data command or in a restart file. -

    -

    N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple dihedral types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of dihedral types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). -

    -

    Note that using a dihedral_coeff command can override a previous setting -for the same dihedral type. For example, these commands set the coeffs -for all dihedral types, then overwrite the coeffs for just dihedral type 2: -

    -
    dihedral_coeff * 80.0 1 3
-dihedral_coeff 2 200.0 1 3 
-
    -

    A line in a data file that specifies dihedral coefficients uses the exact -same format as the arguments of the dihedral_coeff command in an input -script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Dihedral Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as -

    -
    1 80.0 1 3 
-
    -

    The dihedral_style class2 is an exception to -this rule, in that an additional argument is used in the input script -to allow specification of the cross-term coefficients. See its doc -page for details. -

    -

    IMPORTANT NOTE: When comparing the formulas and coefficients for -various LAMMPS dihedral styles with dihedral equations defined by -other force fields, note that some force field implementations -divide/multiply the energy prefactor K by the multiple number of -torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does -not do this, i.e. the listed dihedral equation applies to each -individual dihedral. Thus you need to define K appropriately to -account for this difference if necessary. -

    -
    - -

    Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated dihedral_coeff command. -

    -

    Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -this page. -

    - - -
    - -

    Restrictions: -

    -

    This command must come after the simulation box is defined by a -read_data, read_restart, or -create_box command. -

    -

    A dihedral style must be defined before any dihedral coefficients are -set, either in the input script or in a data file. -

    -

    Related commands: -

    -

    dihedral_style -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_cosine_shift_exp.html b/doc/doc2/dihedral_cosine_shift_exp.html deleted file mode 100644 index b6712072e9..0000000000 --- a/doc/doc2/dihedral_cosine_shift_exp.html +++ /dev/null @@ -1,92 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style cosine/shift/exp command -

    -

    dihedral_style cosine/shift/exp/omp command -

    -

    Syntax: -

    -
    dihedral_style cosine/shift/exp 
-
    -

    Examples: -

    -
    dihedral_style cosine/shift/exp
-dihedral_coeff 1 10.0 45.0 2.0 
-
    -

    Description: -

    -

    The cosine/shift/exp dihedral style uses the potential -

    -
    -
    -

    where Umin, theta, and a are defined for each dihedral type. -

    -

    The potential is bounded between [-Umin:0] and the minimum is located -at the angle theta0. The a parameter can be both positive or negative -and is used to control the spring constant at the equilibrium. -

    -

    The spring constant is given by k=a exp(a) Umin/ [2 (Exp(a)-1)]. -For a>3 k/Umin = a/2 to better than 5% relative error. For negative -values of the a parameter, the spring constant is essentially zero, -and anharmonic terms takes over. The potential is furthermore well -behaved in the limit a->0, where it has been implemented to linear -order in a for a < 0.001. -

    -

    The following coefficients must be defined for each dihedral type via -the dihedral_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • umin (energy) -
    • theta (angle) -
    • A (real number) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff, -angle_cosineshiftexp -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_fourier.html b/doc/doc2/dihedral_fourier.html deleted file mode 100644 index f1b85a1692..0000000000 --- a/doc/doc2/dihedral_fourier.html +++ /dev/null @@ -1,82 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style fourier command -

    -

    dihedral_style fourier/omp command -

    -

    Syntax: -

    -
    dihedral_style fourier 
-
    -

    Examples: -

    -
    dihedral_style fourier
-dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 
-
    -

    Description: -

    -

    The fourier dihedral style uses the potential: -

    -
    -
    -

    The following coefficients must be defined for each dihedral type via the -dihedral_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • m (integer >=1) -
    • K1 (energy) -
    • n1 (integer >= 0) -
    • d1 (degrees) -
    • .... -
    • Km (energy) -
    • nm (integer >= 0) -
    • dm (degrees) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_harmonic.html b/doc/doc2/dihedral_harmonic.html deleted file mode 100644 index b4bc70655d..0000000000 --- a/doc/doc2/dihedral_harmonic.html +++ /dev/null @@ -1,90 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style harmonic command -

    -

    dihedral_style harmonic/omp command -

    -

    Syntax: -

    -
    dihedral_style harmonic 
-
    -

    Examples: -

    -
    dihedral_style harmonic
-dihedral_coeff 1 80.0 1 2 
-
    -

    Description: -

    -

    The harmonic dihedral style uses the potential -

    -
    -
    -

    The following coefficients must be defined for each dihedral type via the -dihedral_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K (energy) -
    • d (+1 or -1) -
    • n (integer >= 0) -
    -

    IMPORTANT NOTE: Here are important points to take note of when -defining LAMMPS dihedral coefficients for the harmonic style, so that -they are compatible with how harmonic dihedrals are defined by other -force fields: -

    -
    • The LAMMPS convention is that the trans position = 180 degrees, while -in some force fields trans = 0 degrees. - -
    • Some force fields reverse the sign convention on d. - -
    • Some force fields let n be positive or negative which corresponds to -d = 1 or -1 for the harmonic style. -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_helix.html b/doc/doc2/dihedral_helix.html deleted file mode 100644 index 461cbb399f..0000000000 --- a/doc/doc2/dihedral_helix.html +++ /dev/null @@ -1,91 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style helix command -

    -

    dihedral_style helix/omp command -

    -

    Syntax: -

    -
    dihedral_style helix 
-
    -

    Examples: -

    -
    dihedral_style helix
-dihedral_coeff 1 80.0 100.0 40.0 
-
    -

    Description: -

    -

    The helix dihedral style uses the potential -

    -
    -
    -

    This coarse-grain dihedral potential is described in (Guo). -For dihedral angles in the helical region, the energy function is -represented by a standard potential consisting of three minima, one -corresponding to the trans (t) state and the other to gauche states -(g+ and g-). The paper describes how the A,B,C parameters are chosen -so as to balance secondary (largely driven by local interactions) and -tertiary structure (driven by long-range interactions). -

    -

    The following coefficients must be defined for each dihedral type via the -dihedral_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • A (energy) -
    • B (energy) -
    • C (energy) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    -
    - - - -

    (Guo) Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996). -

    - diff --git a/doc/doc2/dihedral_hybrid.html b/doc/doc2/dihedral_hybrid.html deleted file mode 100644 index 23960e40c8..0000000000 --- a/doc/doc2/dihedral_hybrid.html +++ /dev/null @@ -1,97 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style hybrid command -

    -

    Syntax: -

    -
    dihedral_style hybrid style1 style2 ... 
-
    -
    • style1,style2 = list of one or more dihedral styles -
    -

    Examples: -

    -
    dihedral_style hybrid harmonic helix
-dihedral_coeff 1 harmonic 6.0 1 3
-dihedral_coeff 2* helix 10 10 10 
-
    -

    Description: -

    -

    The hybrid style enables the use of multiple dihedral styles in one -simulation. An dihedral style is assigned to each dihedral type. For -example, dihedrals in a polymer flow (of dihedral type 1) could be -computed with a harmonic potential and dihedrals in the wall -boundary (of dihedral type 2) could be computed with a helix -potential. The assignment of dihedral type to style is made via the -dihedral_coeff command or in the data file. -

    -

    In the dihedral_coeff commands, the name of a dihedral style must be -added after the dihedral type, with the remaining coefficients being -those appropriate to that style. In the example above, the 2 -dihedral_coeff commands set dihedrals of dihedral type 1 to be -computed with a harmonic potential with coefficients 6.0, 1, 3 for -K, d, n. All other dihedral types (2-N) are computed with a helix -potential with coefficients 10, 10, 10 for A, B, C. -

    -

    If dihedral coefficients are specified in the data file read via the -read_data command, then the same rule applies. -E.g. "harmonic" or "helix", must be added after the dihedral type, for -each line in the "Dihedral Coeffs" section, e.g. -

    -
    Dihedral Coeffs 
-
    -
    1 harmonic 6.0 1 3
-2 helix 10 10 10
-... 
-
    -

    If class2 is one of the dihedral hybrid styles, the same rule holds -for specifying additional AngleTorsion (and EndBondTorsion, etc) -coefficients either via the input script or in the data file. -I.e. class2 must be added to each line after the dihedral type. For -lines in the AngleTorsion (or EndBondTorsion, etc) section of the data -file for dihedral types that are not class2, you must use an -dihedral style of skip as a placeholder, e.g. -

    -
    AngleTorsion Coeffs 
-
    -
    1 skip
-2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0
-... 
-
    -

    Note that it is not necessary to use the dihedral style skip in the -input script, since AngleTorsion (or EndBondTorsion, etc) coefficients -need not be specified at all for dihedral types that are not class2. -

    -

    A dihedral style of none with no additional coefficients can be used -in place of a dihedral style, either in a input script dihedral_coeff -command or in the data file, if you desire to turn off interactions -for specific dihedral types. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Unlike other dihedral styles, the hybrid dihedral style does not store -dihedral coefficient info for individual sub-styles in a binary -restart files. Thus when retarting a simulation from a -restart file, you need to re-specify dihedral_coeff commands. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_multi_harmonic.html b/doc/doc2/dihedral_multi_harmonic.html deleted file mode 100644 index 5557b772b4..0000000000 --- a/doc/doc2/dihedral_multi_harmonic.html +++ /dev/null @@ -1,79 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style multi/harmonic command -

    -

    dihedral_style multi/harmonic/omp command -

    -

    Syntax: -

    -
    dihedral_style multi/harmonic 
-
    -

    Examples: -

    -
    dihedral_style multi/harmonic
-dihedral_coeff 1 20 20 20 20 20 
-
    -

    Description: -

    -

    The multi/harmonic dihedral style uses the potential -

    -
    -
    -

    The following coefficients must be defined for each dihedral type via the -dihedral_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • A1 (energy) -
    • A2 (energy) -
    • A3 (energy) -
    • A4 (energy) -
    • A5 (energy) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_nharmonic.html b/doc/doc2/dihedral_nharmonic.html deleted file mode 100644 index 256ea0651a..0000000000 --- a/doc/doc2/dihedral_nharmonic.html +++ /dev/null @@ -1,79 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style nharmonic command -

    -

    dihedral_style nharmonic/omp command -

    -

    Syntax: -

    -
    dihedral_style nharmonic 
-
    -

    Examples: -

    -
    dihedral_style nharmonic
-dihedral_coeff 3 10.0 20.0 30.0 
-
    -

    Description: -

    -

    The nharmonic dihedral style uses the potential: -

    -
    -
    -

    The following coefficients must be defined for each dihedral type via the -dihedral_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • n (integer >=1) -
    • A1 (energy) -
    • A2 (energy) -
    • ... -
    • An (energy) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_none.html b/doc/doc2/dihedral_none.html deleted file mode 100644 index 439ab77036..0000000000 --- a/doc/doc2/dihedral_none.html +++ /dev/null @@ -1,34 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style none command -

    -

    Syntax: -

    -
    dihedral_style none 
-
    -

    Examples: -

    -
    dihedral_style none 
-
    -

    Description: -

    -

    Using an dihedral style of none means dihedral forces are not -computed, even if quadruplets of dihedral atoms were listed in the -data file read by the read_data command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_opls.html b/doc/doc2/dihedral_opls.html deleted file mode 100644 index 133841c79c..0000000000 --- a/doc/doc2/dihedral_opls.html +++ /dev/null @@ -1,93 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style opls command -

    -

    dihedral_style opls/kk command -

    -

    dihedral_style opls/omp command -

    -

    Syntax: -

    -
    dihedral_style opls 
-
    -

    Examples: -

    -
    dihedral_style opls
-dihedral_coeff 1 1.740 -0.157 0.279 0.00   # CT-CT-CT-CT
-dihedral_coeff 2 0.000 0.000 0.366 0.000   # CT-CT-CT-HC
-dihedral_coeff 3 0.000 0.000 0.318 0.000   # HC-CT-CT-HC 
-
    -

    Description: -

    -

    The opls dihedral style uses the potential -

    -
    -
    -

    Note that the usual 1/2 factor is not included in the K values. -

    -

    This dihedral potential is used in the OPLS force field and is -described in (Watkins). -

    -

    The following coefficients must be defined for each dihedral type via the -dihedral_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: -

    -
    • K1 (energy) -
    • K2 (energy) -
    • K3 (energy) -
    • K4 (energy) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    -
    - - - -

    (Watkins) Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001). -

    - diff --git a/doc/doc2/dihedral_quadratic.html b/doc/doc2/dihedral_quadratic.html deleted file mode 100644 index 2d6ffa43f1..0000000000 --- a/doc/doc2/dihedral_quadratic.html +++ /dev/null @@ -1,80 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style quadratic command -

    -

    dihedral_style quadratic/omp command -

    -

    Syntax: -

    -
    dihedral_style quadratic 
-
    -

    Examples: -

    -
    dihedral_style quadratic
-dihedral_coeff 100.0 80.0 
-
    -

    Description: -

    -

    The quadratic dihedral style uses the potential: -

    -
    -
    -

    This dihedral potential can be used to keep a dihedral in a predefined -value (cis=zero, right-hand convention is used). -

    -

    The following coefficients must be defined for each dihedral type via -the dihedral_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • K (energy/radian^2) -
    • phi0 (degrees) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/dihedral_style.html b/doc/doc2/dihedral_style.html deleted file mode 100644 index 0eb962eadc..0000000000 --- a/doc/doc2/dihedral_style.html +++ /dev/null @@ -1,121 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style command -

    -

    Syntax: -

    -
    dihedral_style style 
-
    -
    • style = none or hybrid or charmm or class2 or harmonic or helix or multi/harmonic or opls -
    -

    Examples: -

    -
    dihedral_style harmonic
-dihedral_style multi/harmonic
-dihedral_style hybrid harmonic charmm 
-
    -

    Description: -

    -

    Set the formula(s) LAMMPS uses to compute dihedral interactions -between quadruplets of atoms, which remain in force for the duration -of the simulation. The list of dihedral quadruplets is read in by a -read_data or read_restart command -from a data or restart file. -

    -

    Hybrid models where dihedrals are computed using different dihedral -potentials can be setup using the hybrid dihedral style. -

    -

    The coefficients associated with a dihedral style can be specified in -a data or restart file or via the dihedral_coeff -command. -

    -

    All dihedral potentials store their coefficient data in binary restart -files which means dihedral_style and -dihedral_coeff commands do not need to be -re-specified in an input script that restarts a simulation. See the -read_restart command for details on how to do -this. The one exception is that dihedral_style hybrid only stores -the list of sub-styles in the restart file; dihedral coefficients need -to be re-specified. -

    -

    IMPORTANT NOTE: When both a dihedral and pair style is defined, the -special_bonds command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 4 bonded atoms. -

    -

    In the formulas listed for each dihedral style, phi is the torsional -angle defined by the quadruplet of atoms. This angle has a sign -convention as shown in this diagram: -

    -
    -
    -

    where the I,J,K,L ordering of the 4 atoms that define the dihedral -is from left to right. -

    -

    This sign convention effects several of the dihedral styles listed -below (e.g. charmm, helix) in the sense that the energy formula -depends on the sign of phi, which may be reflected in the value of the -coefficients you specify. -

    -

    IMPORTANT NOTE: When comparing the formulas and coefficients for -various LAMMPS dihedral styles with dihedral equations defined by -other force fields, note that some force field implementations -divide/multiply the energy prefactor K by the multiple number of -torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does -not do this, i.e. the listed dihedral equation applies to each -individual dihedral. Thus you need to define K appropriately via -the dihedral_coeff command to account for this -difference if necessary. -

    -
    - -

    Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated dihedral_coeff command. -

    -

    Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -this page. -

    - - -
    - -

    Restrictions: -

    -

    Dihedral styles can only be set for atom styles that allow dihedrals -to be defined. -

    -

    Most dihedral styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info on packages. -The doc pages for individual dihedral potentials tell if it is part of -a package. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: -

    -

    dihedral_style none -

    - diff --git a/doc/doc2/dihedral_table.html b/doc/doc2/dihedral_table.html deleted file mode 100644 index 754bac683e..0000000000 --- a/doc/doc2/dihedral_table.html +++ /dev/null @@ -1,211 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dihedral_style table command -

    -

    dihedral_style table/omp command -

    -

    Syntax: -

    -
    dihedral_style table style Ntable 
-
    -
    • style = linear or spline = method of interpolation -
    • Ntable = size of the internal lookup table -
    -

    Examples: -

    -
    dihedral_style table spline 400
-dihedral_style table linear 1000
-dihedral_coeff 1 file.table DIH_TABLE1
-dihedral_coeff 2 file.table DIH_TABLE2 
-
    -

    Description: -

    -

    The table dihedral style creates interpolation tables of length -Ntable from dihedral potential and derivative values listed in a -file(s) as a function of the dihedral angle "phi". The files are read -by the dihedral_coeff command. -

    -

    The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -Ntable dihedral angles. During a simulation, these tables are used -to interpolate energy and force values on individual atoms as -needed. The interpolation is done in one of 2 styles: linear or -spline. -

    -

    For the linear style, the dihedral angle (phi) is used to find 2 -surrounding table values from which an energy or its derivative is -computed by linear interpolation. -

    -

    For the spline style, cubic spline coefficients are computed and -stored at each of the Ntable evenly-spaced values in the -interpolated table. For a given dihedral angle (phi), the appropriate -coefficients are chosen from this list, and a cubic polynomial is used -to compute the energy and the derivative at this angle. -

    -

    The following coefficients must be defined for each dihedral type via -the dihedral_coeff command as in the example -above. -

    -
    • filename -
    • keyword -
    -

    The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. -

    -
    - -

    The format of a tabulated file is as follows (without the -parenthesized comments). It can begin with one or more comment -or blank lines. -

    -
    # Table of the potential and its negative derivative  
-
    -
    DIH_TABLE1                   (keyword is the first text on line)
-N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
-                             (blank line)
-1 -168.0 -1.40351172223 -0.0423346818422
-2 -156.0 -1.70447981034 -0.00811786522531
-3 -144.0 -1.62956100432 0.0184129719987
-...
-30 180.0 -0.707106781187 -0.0719306095245 
-
    -
    # Example 2: table of the potential. Forces omitted 
-
    -
    DIH_TABLE2
-N 30 NOF CHECKU testU.dat CHECKF testF.dat 
-
    -
    1 -168.0 -1.40351172223
-2 -156.0 -1.70447981034
-3 -144.0 -1.62956100432
-...
-30 180.0 -0.707106781187 
-
    -

    A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -dihedral_coeff command. The next line lists (in -any order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. -

    -

    Following a blank line, the next N lines list the tabulated values. On -each line, the 1st value is the index from 1 to N, the 2nd value is -the angle value, the 3rd value is the energy (in energy units), and -the 4th is -dE/d(phi) also in energy units). The 3rd term is the -energy of the 4-atom configuration for the specified angle. The 4th -term (when present) is the negative derivative of the energy with -respect to the angle (in degrees, or radians depending on whether the -user selected DEGREES or RADIANS). Thus the units of the last term -are still energy, not force. The dihedral angle values must increase -from one line to the next. -

    -

    Dihedral table splines are cyclic. There is no discontinuity at 180 -degrees (or at any other angle). Although in the examples above, the -angles range from -180 to 180 degrees, in general, the first angle in -the list can have any value (positive, zero, or negative). However -the range of angles represented in the table must be strictly less -than 360 degrees (2pi radians) to avoid angle overlap. (You may not -supply entries in the table for both 180 and -180, for example.) If -the user's table covers only a narrow range of dihedral angles, -strange numerical behavior can occur in the large remaining gap. -

    -

    Parameters: -

    -

    The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the dihedral_style table command. -Let Ntable is the number of table entries requested dihedral_style -command, and let Nfile be the parameter following "N" in the -tabulated file ("30" in the sparse example above). What LAMMPS does -is a preliminary interpolation by creating splines using the Nfile -tabulated values as nodal points. It uses these to interpolate as -needed to generate energy and derivative values at Ntable different -points (which are evenly spaced over a 360 degree range, even if the -angles in the file are not). The resulting tables of length Ntable -are then used as described above, when computing energy and force for -individual dihedral angles and their atoms. This means that if you -want the interpolation tables of length Ntable to match exactly what -is in the tabulated file (with effectively nopreliminary -interpolation), you should set Ntable = Nfile. To insure the -nodal points in the user's file are aligned with the interpolated -table entries, the angles in the table should be integer multiples of -360/Ntable degrees, or 2*PI/Ntable radians (depending on your -choice of angle units). -

    -

    The optional "NOF" keyword allows the user to omit the forces -(negative energy derivatives) from the table file (normally located in -the 4th column). In their place, forces will be calculated -automatically by differentiating the potential energy function -indicated by the 3rd column of the table (using either linear or -spline interpolation). -

    -

    The optional "DEGREES" keyword allows the user to specify angles in -degrees instead of radians (default). -

    -

    The optional "RADIANS" keyword allows the user to specify angles in -radians instead of degrees. (Note: This changes the way the forces -are scaled in the 4th column of the data file.) -

    -

    The optional "CHECKU" keyword is followed by a filename. This allows -the user to save all of the the Ntable different entries in the -interpolated energy table to a file to make sure that the interpolated -function agrees with the user's expectations. (Note: You can -temporarily increase the Ntable parameter to a high value for this -purpose. "Ntable" is explained above.) -

    -

    The optional "CHECKF" keyword is analogous to the "CHECKU" keyword. -It is followed by a filename, and it allows the user to check the -interpolated force table. This option is available even if the user -selected the "NOF" option. -

    -

    Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds one -that matches the specified keyword. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restrictions: -

    -

    This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    dihedral_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/dimension.html b/doc/doc2/dimension.html deleted file mode 100644 index 65099ab255..0000000000 --- a/doc/doc2/dimension.html +++ /dev/null @@ -1,53 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dimension command -

    -

    Syntax: -

    -
    dimension N 
-
    -
    • N = 2 or 3 -
    -

    Examples: -

    -
    dimension 2 
-
    -

    Description: -

    -

    Set the dimensionality of the simulation. By default LAMMPS runs 3d -simulations. To run a 2d simulation, this command should be used -prior to setting up a simulation box via the -create_box or read_data commands. -Restart files also store this setting. -

    -

    See the discussion in Section_howto for -additional instructions on how to run 2d simulations. -

    -

    IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size -spheres or ellipsoids, as opposed to point particles. In 2d, the -particles will still be spheres or ellipsoids, not circular disks or -ellipses, meaning their moment of inertia will be the same as in 3d. -

    -

    Restrictions: -

    -

    This command must be used before the simulation box is defined by a -read_data or create_box command. -

    -

    Related commands: -

    -

    fix enforce2d -

    -

    Default: -

    -
    dimension 3 
-
    - diff --git a/doc/doc2/displace_atoms.html b/doc/doc2/displace_atoms.html deleted file mode 100644 index 1c3aa5ece1..0000000000 --- a/doc/doc2/displace_atoms.html +++ /dev/null @@ -1,143 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    displace_atoms command -

    -

    Syntax: -

    -
    displace_atoms group-ID style args keyword value ... 
-
    -
    • group-ID = ID of group of atoms to displace - -
    • style = move or ramp or random or rotate - -
        move args = delx dely delz
-    delx,dely,delz = distance to displace in each dimension (distance units)
-    any of delx,dely,delz can be a variable (see below)
-  ramp args = ddim dlo dhi dim clo chi
-    ddim = x or y or z
-    dlo,dhi = displacement distance between dlo and dhi (distance units)
-    dim = x or y or z
-    clo,chi = lower and upper bound of domain to displace (distance units)
-  random args = dx dy dz seed
-    dx,dy,dz = random displacement magnitude in each dimension (distance units)
-    seed = random # seed (positive integer)
-  rotate args = Px Py Pz Rx Ry Rz theta
-    Px,Py,Pz = origin point of axis of rotation (distance units)
-    Rx,Ry,Rz = axis of rotation vector
-    theta = angle of rotation (degrees) 
-
      -
    • zero or more keyword/value pairs may be appended - -
        keyword = units
-    value = box or lattice 
-
      - -
    -

    Examples: -

    -
    displace_atoms top move 0 -5 0 units box
-displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 
-
    -

    Description: -

    -

    Displace a group of atoms. This can be used to move atoms a large -distance before beginning a simulation or to randomize atoms initially -on a lattice. For example, in a shear simulation, an initial strain -can be imposed on the system. Or two groups of atoms can be brought -into closer proximity. -

    -

    The move style displaces the group of atoms by the specified 3d -displacement vector. Any of the 3 quantities defining the vector -components can be specified as an equal-style or atom-style -variable. If the value is a variable, it should be -specified as v_name, where name is the variable name. In this case, -the variable will be evaluated, and its value(s) used for the -displacement(s). The scale factor implied by the units keyword will -also be applied to the variable result. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Atom-style variables can specify the same formulas as -equal-style variables but can also include per-atom values, such as -atom coordinates or per-atom values read from a file. Note that if -the variable references other compute or fix -commands, those values must be up-to-date for the current timestep. -See the "Variable Accuracy" section of the variable -doc page for more details. -

    -

    The ramp style displaces atoms a variable amount in one dimension -depending on the atom's coordinate in a (possibly) different -dimension. For example, the second example command displaces atoms in -the x-direction an amount between 0.0 and 5.0 distance units. Each -atom's displacement depends on the fractional distance its y -coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside -those bounds will be moved the minimum (0.0) or maximum (5.0) amount. -

    -

    The random style independently moves each atom in the group by a -random displacement, uniformly sampled from a value between -dx and -+dx in the x dimension, and similarly for y and z. Random numbers are -used in such a way that the displacement of a particular atom is the -same, regardless of how many processors are being used. -

    -

    The rotate style rotates each atom in the group by the angle theta -around a rotation axis R = (Rx,Ry,Rz) that goes thru a point P = -(Px,Py,Pz). The direction of rotation for the atoms around the -rotation axis is consistent with the right-hand rule: if your -right-hand's thumb points along R, then your fingers wrap around the -axis in the direction of positive theta. -

    -

    Distance units for displacements and the origin point of the rotate -style are determined by the setting of box or lattice for the -units keyword. Box means distance units as defined by the -units command - e.g. Angstroms for real units. -Lattice means distance units are in lattice spacings. The -lattice command must have been previously used to -define the lattice spacing. -

    -
    - -

    IMPORTANT NOTE: Care should be taken not to move atoms on top of other -atoms. After the move, atoms are remapped into the periodic -simulation box if needed, and any shrink-wrap boundary conditions (see -the boundary command) are enforced which may change -the box size. Other than this effect, this command does not change -the size or shape of the simulation box. See the -change_box command if that effect is desired. -

    -

    IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this -command. If the simulation box is non-periodic and shrink-wrapped -(see the boundary command), this can change its size -or shape. This is not a problem, except that the mapping of -processors to the simulation box is not changed by this command from -its initial 3d configuration; see the processors -command. Thus, if the box size/shape changes dramatically, the -mapping of processors to the simulation box may not end up as optimal -as the initial mapping attempted to be. -

    -
    - -

    Restrictions: -

    -

    You cannot rotate around any rotation vector except the z-axis for a -2d simulation. -

    -

    Related commands: -

    -

    lattice, change_box, -fix_move -

    -

    Default: -

    -

    The option defaults are units = lattice. -

    - diff --git a/doc/doc2/dump.html b/doc/doc2/dump.html deleted file mode 100644 index 08d97ed84a..0000000000 --- a/doc/doc2/dump.html +++ /dev/null @@ -1,649 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dump command -

    -

    dump h5md command -

    -

    dump image command -

    -

    dump movie command -

    -

    dump molfile command -

    -

    Syntax: -

    -
    dump ID group-ID style N file args 
-
    -
    • ID = user-assigned name for the dump - -
    • group-ID = ID of the group of atoms to be dumped - -
    • style = atom or atom/gz or atom/mpiio or cfg or cfg/gz or cfg/mpiio or dcd or xtc or xyz or xyz/gz or xyz/mpiio or h5md or image or movie or molfile or local or custom or custom/gz or custom/mpiio - -
    • N = dump every this many timesteps - -
    • file = name of file to write dump info to - -
    • args = list of arguments for a particular style - -
        atom args = none
-  atom/gz args = none
-  atom/mpiio args = none
-  cfg args = same as custom args, see below
-  cfg/gz args = same as custom args, see below
-  cfg/mpiio args = same as custom args, see below
-  dcd args = none
-  xtc args = none
-  xyz args = none 
-
      -
        xyz/gz args = none 
-
      -
        xyz/mpiio args = none 
-
      -
        h5md args = discussed on dump h5md doc page 
-
      -
        image args = discussed on dump image doc page 
-
      -
        movie args = discussed on dump image doc page 
-
      -
        molfile args = discussed on dump molfile doc page 
-
      -
        local args = list of local attributes
-    possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
-      index = enumeration of local values
-      c_ID = local vector calculated by a compute with ID
-      c_ID[N] = Nth column of local array calculated by a compute with ID
-      f_ID = local vector calculated by a fix with ID
-      f_ID[N] = Nth column of local array calculated by a fix with ID 
-
      -
        custom or custom/gz or custom/mpiio args = list of atom attributes
-    possible attributes = id, mol, proc, procp1, type, element, mass,
-			  x, y, z, xs, ys, zs, xu, yu, zu, 
-			  xsu, ysu, zsu, ix, iy, iz,
-			  vx, vy, vz, fx, fy, fz,
-                          q, mux, muy, muz, mu,
-                          radius, diameter, omegax, omegay, omegaz,
-			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
-			  c_ID, c_ID[N], f_ID, f_ID[N], v_name 
-
      -
            id = atom ID
-      mol = molecule ID
-      proc = ID of processor that owns atom
-      procp1 = ID+1 of processor that owns atom
-      type = atom type
-      element = name of atom element, as defined by dump_modify command
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      xsu,ysu,zsu = scaled unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipole moment of atom
-      mu = magnitude of dipole moment of atom
-      radius,diameter = radius,diameter of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      tqx,tqy,tqz = torque on finite-size particles
-      c_ID = per-atom vector calculated by a compute with ID
-      c_ID[N] = Nth column of per-atom array calculated by a compute with ID
-      f_ID = per-atom vector calculated by a fix with ID
-      f_ID[N] = Nth column of per-atom array calculated by a fix with ID
-      v_name = per-atom vector calculated by an atom-style variable with name
-      d_name = per-atom floating point vector with name, managed by fix property/atom
-      i_name = per-atom integer vector with name, managed by fix property/atom 
-
      - -
    -

    Examples: -

    -
    dump myDump all atom 100 dump.atom
-dump myDump all atom/mpiio 100 dump.atom.mpiio
-dump myDump all atom/gz 100 dump.atom.gz
-dump 2 subgroup atom 50 dump.run.bin
-dump 2 subgroup atom 50 dump.run.mpiio.bin
-dump 4a all custom 100 dump.myforce.* id type x y vx fx
-dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
-dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
-dump 1 all xtc 1000 file.xtc 
-
    -

    Description: -

    -

    Dump a snapshot of atom quantities to one or more files every N -timesteps in one of several styles. The image and movie styles are -the exception: the image style renders a JPG, PNG, or PPM image file -of the atom configuration every N timesteps while the movie style -combines and compresses them into a movie file; both are discussed in -detail on the dump image doc page. The timesteps on -which dump output is written can also be controlled by a variable. -See the dump_modify every command. -

    -

    Only information for atoms in the specified group is dumped. The -dump_modify thresh and region commands can also -alter what atoms are included. Not all styles support all these -options; see details below. -

    -

    As described below, the filename determines the kind of output (text -or binary or gzipped, one big file or one per timestep, one big file -or multiple smaller files). -

    -

    IMPORTANT NOTE: Because periodic boundary conditions are enforced only -on timesteps when neighbor lists are rebuilt, the coordinates of an -atom written to a dump file may be slightly outside the simulation -box. -

    -

    IMPORTANT NOTE: Unless the dump_modify sort option -is invoked, the lines of atom information written to dump files -(typically one line per atom) will be in an indeterminate order for -each snapshot. This is even true when running on a single processor, -if the atom_modify sort option is on, which it is -by default. In this case atoms are re-ordered periodically during a -simulation, due to spatial sorting. It is also true when running in -parallel, because data for a single snapshot is collected from -multiple processors, each of which owns a subset of the atoms. -

    -

    For the atom, custom, cfg, and local styles, sorting is off by -default. For the dcd, xtc, xyz, and molfile styles, sorting by -atom ID is on by default. See the dump_modify doc -page for details. -

    -

    The atom/gz, cfg/gz, custom/gz, and xyz/gz styles are identical -in command syntax to the corresponding styles without "gz", however, -they generate compressed files using the zlib library. Thus the filename -suffix ".gz" is mandatory. This is an alternative approach to writing -compressed files via a pipe, as done by the regular dump styles, which -may be required on clusters where the interface to the high-speed network -disallows using the fork() library call (which is needed for a pipe). -For the remainder of this doc page, you should thus consider the atom -and atom/gz styles (etc) to be inter-changeable, with the exception -of the required filename suffix. -

    -

    As explained below, the atom/mpiio, cfg/mpiio, custom/mpiio, and -xyz/mpiio styles are identical in command syntax and in the format -of the dump files they create, to the corresponding styles without -"mpiio", except the single dump file they produce is written in -parallel via the MPI-IO library. For the remainder of this doc page, -you should thus consider the atom and atom/mpiio styles (etc) to -be inter-changeable. The one exception is how the filename is -specified for the MPI-IO styles, as explained below. -

    -
    - -

    The style keyword determines what atom quantities are written to the -file and in what format. Settings made via the -dump_modify command can also alter the format of -individual values and the file itself. -

    -

    The atom, local, and custom styles create files in a simple text -format that is self-explanatory when viewing a dump file. Many of the -LAMMPS post-processing tools, including -Pizza.py, work with this -format, as does the rerun command. -

    -

    For post-processing purposes the atom, local, and custom text -files are self-describing in the following sense. -

    -

    The dimensions of the simulation box are included in each snapshot. -For an orthogonal simulation box this information is is formatted as: -

    -
    ITEM: BOX BOUNDS xx yy zz
-xlo xhi
-ylo yhi
-zlo zhi 
-
    -

    where xlo,xhi are the maximum extents of the simulation box in the -x-dimension, and similarly for y and z. The "xx yy zz" represent 6 -characters that encode the style of boundary for each of the 6 -simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of -the 6 characters is either p = periodic, f = fixed, s = shrink wrap, -or m = shrink wrapped with a minimum value. See the -boundary command for details. -

    -

    For triclinic simulation boxes (non-orthogonal), an orthogonal -bounding box which encloses the triclinic simulation box is output, -along with the 3 tilt factors (xy, xz, yz) of the triclinic box, -formatted as follows: -

    -
    ITEM: BOX BOUNDS xy xz yz xx yy zz 
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz 
-
    -

    The presence of the text "xy xz yz" in the ITEM line indicates that -the 3 tilt factors will be included on each of the 3 following lines. -This bounding box is convenient for many visualization programs. The -meaning of the 6 character flags for "xx yy zz" is the same as above. -

    -

    Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they repesent a bounding box. See this -section of the doc pages for a geometric -description of triclinic boxes, as defined by LAMMPS, simple formulas -for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are -calculated from the triclinic parameters, and how to transform those -parameters to and from other commonly used triclinic representations. -

    -

    The "ITEM: ATOMS" line in each snapshot lists column descriptors for -the per-atom lines that follow. For example, the descriptors would be -"id type xs ys zs" for the default atom style, and would be the atom -attributes you specify in the dump command for the custom style. -

    -

    For style atom, atom coordinates are written to the file, along with -the atom ID and atom type. By default, atom coords are written in a -scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom -is at a location 1/4 of the distance from xlo to xhi of the box -boundaries. The format can be changed to unscaled coords via the -dump_modify settings. Image flags can also be -added for each atom via dump_modify. -

    -

    Style custom allows you to specify a list of atom attributes to be -written to the dump file for each atom. Possible attributes are -listed above and will appear in the order specified. You cannot -specify a quantity that is not defined for a particular simulation - -such as q for atom style bond, since that atom style doesn't -assign charges. Dumps occur at the very end of a timestep, so atom -attributes will include effects due to fixes that are applied during -the timestep. An explanation of the possible dump custom attributes -is given below. -

    -

    For style local, local output generated by computes -and fixes is used to generate lines of output that is -written to the dump file. This local data is typically calculated by -each processor based on the atoms it owns, but there may be zero or -more entities per atom, e.g. a list of bond distances. An explanation -of the possible dump local attributes is given below. Note that by -using input from the compute -property/local command with dump local, -it is possible to generate information on bonds, angles, etc that can -be cut and pasted directly into a data file read by the -read_data command. -

    -

    Style cfg has the same command syntax as style custom and writes -extended CFG format files, as used by the -AtomEye visualization -package. Since the extended CFG format uses a single snapshot of the -system per file, a wildcard "*" must be included in the filename, as -discussed below. The list of atom attributes for style cfg must -begin with either "mass type xs ys zs" or "mass type xsu ysu zsu" -since these quantities are needed to write the CFG files in the -appropriate format (though the "mass" and "type" fields do not appear -explicitly in the file). Any remaining attributes will be stored as -"auxiliary properties" in the CFG files. Note that you will typically -want to use the dump_modify element command with -CFG-formatted files, to associate element names with atom types, so -that AtomEye can render atoms appropriately. When unwrapped -coordinates xsu, ysu, and zsu are requested, the nominal AtomEye -periodic cell dimensions are expanded by a large factor UNWRAPEXPAND = -10.0, which ensures atoms that are displayed correctly for up to -UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond -this, AtomEye will rewrap the unwrapped coordinates. The expansion -causes the atoms to be drawn farther away from the viewer, but it is -easy to zoom the atoms closer, and the interatomic distances are -unaffected. -

    -

    The dcd style writes DCD files, a standard atomic trajectory format -used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD -files are binary and thus may not be portable to different machines. -The number of atoms per snapshot cannot change with the dcd style. -The unwrap option of the dump_modify command -allows DCD coordinates to be written "unwrapped" by the image flags -for each atom. Unwrapped means that if the atom has passed through -a periodic boundary one or more times, the value is printed for what -the coordinate would be if it had not been wrapped back into the -periodic box. Note that these coordinates may thus be far outside -the box size stored with the snapshot. -

    -

    The xtc style writes XTC files, a compressed trajectory format used -by the GROMACS molecular dynamics package, and described -here. -The precision used in XTC files can be adjusted via the -dump_modify command. The default value of 1000 -means that coordinates are stored to 1/1000 nanometer accuracy. XTC -files are portable binary files written in the NFS XDR data format, -so that any machine which supports XDR should be able to read them. -The number of atoms per snapshot cannot change with the xtc style. -The unwrap option of the dump_modify command allows -XTC coordinates to be written "unwrapped" by the image flags for each -atom. Unwrapped means that if the atom has passed thru a periodic -boundary one or more times, the value is printed for what the -coordinate would be if it had not been wrapped back into the periodic -box. Note that these coordinates may thus be far outside the box size -stored with the snapshot. -

    -

    The xyz style writes XYZ files, which is a simple text-based -coordinate format that many codes can read. Specifically it has -a line with the number of atoms, then a comment line that is -usually ignored followed by one line per atom with the atom type -and the x-, y-, and z-coordinate of that atom. You can use the -dump_modify element option to change the output -from using the (numerical) atom type to an element name (or some -other label). This will help many visualization programs to guess -bonds and colors. -

    -

    Note that atom, custom, dcd, xtc, and xyz style dump files -can be read directly by VMD, a -popular molecular viewing program. See Section -tools of the manual and the -tools/lmp2vmd/README.txt file for more information about support in -VMD for reading and visualizing LAMMPS dump files. -

    -
    - -

    Dumps are performed on timesteps that are a multiple of N (including -timestep 0) and on the last timestep of a minimization if the -minimization converges. Note that this means a dump will not be -performed on the initial timestep after the dump command is invoked, -if the current timestep is not a multiple of N. This behavior can be -changed via the dump_modify first command, which -can also be useful if the dump command is invoked after a minimization -ended on an arbitrary timestep. N can be changed between runs by -using the dump_modify every command (not allowed -for dcd style). The dump_modify every command -also allows a variable to be used to determine the sequence of -timesteps on which dump files are written. In this mode a dump on the -first timestep of a run will also not be written unless the -dump_modify first command is used. -

    -

    The specified filename determines how the dump file(s) is written. -The default is to write one large text file, which is opened when the -dump command is invoked and closed when an undump -command is used or when LAMMPS exits. For the dcd and xtc styles, -this is a single large binary file. -

    -

    Dump filenames can contain two wildcard characters. If a "*" -character appears in the filename, then one file per snapshot is -written and the "*" character is replaced with the timestep value. -For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000, -tmp.dump.20000, etc. This option is not available for the dcd and -xtc styles. Note that the dump_modify pad -command can be used to insure all timestep numbers are the same length -(e.g. 00010), which can make it easier to read a series of dump files -in order with some post-processing tools. -

    -

    If a "%" character appears in the filename, then each of P processors -writes a portion of the dump file, and the "%" character is replaced -with the processor ID from 0 to P-1. For example, tmp.dump.% becomes -tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller -files and can be a fast mode of output on parallel machines that -support parallel I/O for output. This option is not available for the -dcd, xtc, and xyz styles. -

    -

    By default, P = the number of processors meaning one file per -processor, but P can be set to a smaller value via the nfile or -fileper keywords of the dump_modify command. -These options can be the most efficient way of writing out dump files -when running on large numbers of processors. -

    -

    Note that using the "*" and "%" characters together can produce a -large number of small dump files! -

    -

    For the atom/mpiio, cfg/mpiio, custom/mpiio, and xyz/mpiio -styles, a single dump file is written in parallel via the MPI-IO -library, which is part of the MPI standard for versions 2.0 and above. -Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO -package installed, e.g. -

    -
    make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform 
-
    -

    Second, use a dump filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO restart files, which must be both written and read using -MPI-IO, the dump files produced by these MPI-IO styles are identical -in format to the files produced by their non-MPI-IO style -counterparts. This means you can write a dump file using MPI-IO and -use the read_dump command or perform other -post-processing, just as if the dump file was not written using -MPI-IO. -

    -

    Note that MPI-IO dump files are one large file which all processors -write to. You thus cannot use the "%" wildcard character described -above in the filename since that specifies generation of multiple -files. You can use the ".bin" suffix described below in an MPI-IO -dump file; again this file will be written in parallel and have the -same binary format as if it were written without MPI-IO. -

    -

    If the filename ends with ".bin", the dump file (or files, if "*" or -"%" is also used) is written in binary format. A binary dump file -will be about the same size as a text version, but will typically -write out much faster. Of course, when post-processing, you will need -to convert it back to text format (see the binary2txt -tool) or write your own code to read the -binary file. The format of the binary file can be understood by -looking at the tools/binary2txt.cpp file. This option is only -available for the atom and custom styles. -

    -

    If the filename ends with ".gz", the dump file (or files, if "*" or "%" -is also used) is written in gzipped format. A gzipped dump file will -be about 3x smaller than the text version, but will also take longer -to write. This option is not available for the dcd and xtc -styles. -

    -
    - -

    This section explains the local attributes that can be specified as -part of the local style. -

    -

    The index attribute can be used to generate an index number from 1 -to N for each line written into the dump file, where N is the total -number of local datums from all processors, or lines of output that -will appear in the snapshot. Note that because data from different -processors depend on what atoms they currently own, and atoms migrate -between processor, there is no guarantee that the same index will be -used for the same info (e.g. a particular bond) in successive -snapshots. -

    -

    The c_ID and c_ID[N] attributes allow local vectors or arrays -calculated by a compute to be output. The ID in the -attribute should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -compute command for details. There are computes for -calculating local information such as indices, types, and energies for -bonds and angles. -

    -

    Note that computes which calculate global or per-atom quantities, as -opposed to local quantities, cannot be output in a dump local command. -Instead, global quantities can be output by the thermo_style -custom command, and per-atom quantities can be -output by the dump custom command. -

    -

    If c_ID is used as a attribute, then the local vector calculated by -the compute is printed. If c_ID[N] is used, then N must be in the -range from 1-M, which will print the Nth column of the M-length local -array calculated by the compute. -

    -

    The f_ID and f_ID[N] attributes allow local vectors or arrays -calculated by a fix to be output. The ID in the attribute -should be replaced by the actual ID of the fix that has been defined -previously in the input script. -

    -

    If f_ID is used as a attribute, then the local vector calculated by -the fix is printed. If f_ID[N] is used, then N must be in the -range from 1-M, which will print the Nth column of the M-length local -array calculated by the fix. -

    -

    Here is an example of how to dump bond info for a system, -including the distance and energy of each bond: -

    -
    compute 1 all property/local batom1 batom2 btype 
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] 
-
    -
    - -

    This section explains the atom attributes that can be specified as -part of the custom and cfg styles. -

    -

    The id, mol, proc, procp1, type, element, mass, vx, -vy, vz, fx, fy, fz, q attributes are self-explanatory. -

    -

    Id is the atom ID. Mol is the molecule ID, included in the data -file for molecular systems. Proc is the ID of the processor (0 to -Nprocs-1) that currently owns the atom. Procp1 is the proc ID+1, -which can be convenient in place of a type attribute (1 to Ntypes) -for coloring atoms in a visualization program. Type is the atom -type (1 to Ntypes). Element is typically the chemical name of an -element, which you must assign to each type via the dump_modify -element command. More generally, it can be any -string you wish to associated with an atom type. Mass is the atom -mass. Vx, vy, vz, fx, fy, fz, and q are components of -atom velocity and force and atomic charge. -

    -

    There are several options for outputting atom coordinates. The x, -y, z attributes write atom coordinates "unscaled", in the -appropriate distance units (Angstroms, sigma, etc). Use -xs, ys, zs if you want the coordinates "scaled" to the box size, -so that each value is 0.0 to 1.0. If the simulation box is triclinic -(tilted), then all atom coords will still be between 0.0 and 1.0. Use -xu, yu, zu if you want the coordinates "unwrapped" by the image -flags for each atom. Unwrapped means that if the atom has passed thru -a periodic boundary one or more times, the value is printed for what -the coordinate would be if it had not been wrapped back into the -periodic box. Note that using xu, yu, zu means that the -coordinate values may be far outside the box bounds printed with the -snapshot. Using xsu, ysu, zsu is similar to using xu, yu, zu, -except that the unwrapped coordinates are scaled by the box size. Atoms -that have passed through a periodic boundary will have the corresponding -cooordinate increased or decreased by 1.0. -

    -

    The image flags can be printed directly using the ix, iy, iz -attributes. For periodic dimensions, they specify which image of the -simulation box the atom is considered to be in. An image of 0 means -it is inside the box as defined. A value of 2 means add 2 box lengths -to get the true value. A value of -1 means subtract 1 box length to -get the true value. LAMMPS updates these flags as atoms cross -periodic boundaries during the simulation. -

    -

    The mux, muy, muz attributes are specific to dipolar systems -defined with an atom style of dipole. They give the orientation of -the atom's point dipole moment. The mu attribute gives the -magnitude of the atom's dipole moment. -

    -

    The radius and diameter attributes are specific to spherical -particles that have a finite size, such as those defined with an atom -style of sphere. -

    -

    The omegax, omegay, and omegaz attributes are specific to -finite-size spherical particles that have an angular velocity. Only -certain atom styles, such as sphere define this quantity. -

    -

    The angmomx, angmomy, and angmomz attributes are specific to -finite-size aspherical particles that have an angular momentum. Only -the ellipsoid atom style defines this quantity. -

    -

    The tqx, tqy, tqz attributes are for finite-size particles that -can sustain a rotational torque due to interactions with other -particles. -

    -

    The c_ID and c_ID[N] attributes allow per-atom vectors or arrays -calculated by a compute to be output. The ID in the -attribute should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -compute command for details. There are computes for -calculating the per-atom energy, stress, centro-symmetry parameter, -and coordination number of individual atoms. -

    -

    Note that computes which calculate global or local quantities, as -opposed to per-atom quantities, cannot be output in a dump custom -command. Instead, global quantities can be output by the -thermo_style custom command, and local quantities -can be output by the dump local command. -

    -

    If c_ID is used as a attribute, then the per-atom vector calculated -by the compute is printed. If c_ID[N] is used, then N must be in -the range from 1-M, which will print the Nth column of the M-length -per-atom array calculated by the compute. -

    -

    The f_ID and f_ID[N] attributes allow vector or array per-atom -quantities calculated by a fix to be output. The ID in the -attribute should be replaced by the actual ID of the fix that has been -defined previously in the input script. The fix -ave/atom command is one that calculates per-atom -quantities. Since it can time-average per-atom quantities produced by -any compute, fix, or atom-style -variable, this allows those time-averaged results to -be written to a dump file. -

    -

    If f_ID is used as a attribute, then the per-atom vector calculated -by the fix is printed. If f_ID[N] is used, then N must be in the -range from 1-M, which will print the Nth column of the M-length -per-atom array calculated by the fix. -

    -

    The v_name attribute allows per-atom vectors calculated by a -variable to be output. The name in the attribute -should be replaced by the actual name of the variable that has been -defined previously in the input script. Only an atom-style variable -can be referenced, since it is the only style that generates per-atom -values. Variables of style atom can reference individual atom -attributes, per-atom atom attributes, thermodynamic keywords, or -invoke other computes, fixes, or variables when they are evaluated, so -this is a very general means of creating quantities to output to a -dump file. -

    -

    The d_name and i_name attributes allow to output custom per atom -floating point or integer properties that are managed by -fix property/atom. -

    -

    See Section_modify of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. -

    -
    - -

    Restrictions: -

    -

    To write gzipped dump files, you must either compile LAMMPS with the --DLAMMPS_GZIP option or use the styles from the COMPRESS package -- see the Making LAMMPS section of -the documentation. -

    -

    The atom/gz, cfg/gz, custom/gz, and xyz/gz styles are part -of the COMPRESS package. They are only enabled if LAMMPS was built -with that package. See the Making -LAMMPS section for more info. -

    -

    The atom/mpiio, cfg/mpiio, custom/mpiio, and xyz/mpiio styles -are part of the MPIIO package. They are only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    The xtc style is part of the XTC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. This is -because some machines may not support the low-level XDR data format -that XTC files are written with, which will result in a compile-time -error when a low-level include file is not found. Putting this style -in a package makes it easy to exclude from a LAMMPS build for those -machines. However, the XTC package also includes two compatibility -header files and associated functions, which should be a suitable -substitute on machines that do not have the appropriate native header -files. This option can be invoked at build time by adding --DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level -Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has -been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L -machines and should also work on IBM BG/P, and Windows XP/Vista/7 -machines. -

    -

    Related commands: -

    -

    dump h5md, dump image, -dump molfile, dump_modify, -undump -

    -

    Default: -

    -

    The defaults for the image and movie styles are listed on the -dump image doc page. -

    - diff --git a/doc/doc2/dump_h5md.html b/doc/doc2/dump_h5md.html deleted file mode 100644 index 0c6db43234..0000000000 --- a/doc/doc2/dump_h5md.html +++ /dev/null @@ -1,136 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dump h5md command -

    -

    Syntax: -

    -
    dump ID group-ID h5md N file.h5 args 
-
    -
    • ID = user-assigned name for the dump - -
    • group-ID = ID of the group of atoms to be imaged - -
    • h5md = style of dump command (other styles atom or cfg or dcd or xtc or xyz or local or custom are discussed on the dump doc page) - -
    • N = dump every this many timesteps - -
    • file.h5 = name of file to write to - -
    • args = list of data elements to dump, with their dump "subintervals". -At least one element must be given and image may only be present if -position is specified first. - -
        position options
-  image
-  velocity options
-  force options
-  species options
-  file_from ID: do not open a new file, re-use the already opened file from dump ID
-  box value = yes or no
-  create_group value = yes or no
-  author value = quoted string 
-
      -

      For the elements position, velocity, force and species, one -may specify a sub-interval to write the data only every N_element -iterations of the dump (i.e. every N*N_element time steps). This is -specified by the option -

      -
        every N_element 
-
      -

      that follows directly the element declaration. -

      - -
    -

    Examples: -

    -
    dump h5md1 all h5md 100 dump_h5md.h5 position image
-dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
-dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" 
-
    -

    Description: -

    -

    Dump a snapshot of atom coordinates every N timesteps in the -HDF5 based H5MD file format (de Buyl). -HDF5 files are binary, portable and self-describing. This dump style -will write only one file, on the root node. -

    -

    Several dumps may write to the same file, by using file_from and -referring to a previously defined dump. Several groups may also be -stored within the same file by defining several dumps. A dump that -refers (via file_from) to an already open dump ID and that concerns -another particle group must specify create_group yes. -

    - - -

    Each data element is written every N*N_element steps. For image, no -subinterval is needed as it must be present at the same interval as -position. image must be given after position in any case. The -box information (edges in each dimension) is stored at the same -interval than the position element, if present. Else it is stored -every N steps. -

    -

    IMPORTANT NOTE: Because periodic boundary conditions are enforced only -on timesteps when neighbor lists are rebuilt, the coordinates of an -atom written to a dump file may be slightly outside the simulation -box. -

    -

    Use from write_dump: -

    -

    It is possible to use this dump style with the -write_dump command. In this case, the subintervals -must not be set at all. The write_dump command can be used either to -create a new file or to add current data to an existing dump file by -using the file_from keyword. -

    -

    Typically, the species data is fixed. The following two commands -store the position data every 100 timesteps, with the image data, and -store once the species data in the same file. -

    -
    dump h5md1 all h5md 100 dump.h5 position image
-write_dump all h5md dump.h5 file_from h5md1 species 
-
    -
    - -

    Restrictions: -

    -

    The number of atoms per snapshot cannot change with the h5md style. -The position data is stored wrapped (box boundaries not enforced, see -note above). Only orthogonal domains are currently supported. This is -a limitation of the present dump h5md command and not of H5MD itself. -

    -

    The h5md dump style is part of the USER-H5MD package. It is only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. It also -requires (i) building the ch5md library provided with LAMMPS (See the -Making LAMMPS section for more info.) and -(ii) having the HDF5 library installed (C bindings are -sufficient) on your system. The library ch5md is compiled with the -h5cc wrapper provided by the HDF5 library. -

    - - -
    - -

    Related commands: -

    -

    dump, dump_modify, undump -

    -
    - - - -

    (de Buyl) de Buyl, Colberg and Hofling, H5MD: A structured, -efficient, and portable file format for molecular data, -Comp. Phys. Comm. 185(6), 1546-1553 (2014) - -[arXiv:1308.6382]. -

    - diff --git a/doc/doc2/dump_image.html b/doc/doc2/dump_image.html deleted file mode 100644 index c2babe4f63..0000000000 --- a/doc/doc2/dump_image.html +++ /dev/null @@ -1,566 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dump image command -

    -

    dump movie command -

    -

    Syntax: -

    -
    dump ID group-ID style N file color diameter keyword value ... 
-
    -
    • ID = user-assigned name for the dump - -
    • group-ID = ID of the group of atoms to be imaged - -
    • style = image or movie = style of dump command (other styles atom or cfg or dcd or xtc or xyz or local or custom are discussed on the dump doc page) - -
    • N = dump every this many timesteps - -
    • file = name of file to write image to - -
    • color = atom attribute that determines color of each atom - -
    • diameter = atom attribute that determines size of each atom - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = adiam or atom or bond or size or view or center or up or zoom or persp or box or axes or subbox or shiny or ssao - -
        adiam value = number = numeric value for atom diameter (distance units)
-  atom = yes/no = do or do not draw atoms
-  bond values = color width = color and width of bonds
-    color = atom or type or none
-    width = number or atom or type or none
-      number = numeric value for bond width (distance units)
-  size values = width height = size of images
-    width = width of image in # of pixels
-    height = height of image in # of pixels
-  view values = theta phi = view of simulation box
-    theta = view angle from +z axis (degrees)
-    phi = azimuthal view angle (degrees)
-    theta or phi can be a variable (see below)
-  center values = flag Cx Cy Cz = center point of image
-    flag = "s" for static, "d" for dynamic
-    Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
-    Cx,Cy,Cz can be variables (see below)
-  up values = Ux Uy Uz = direction that is "up" in image
-    Ux,Uy,Uz = components of up vector
-    Ux,Uy,Uz can be variables (see below)
-  zoom value = zfactor = size that simulation box appears in image
-    zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
-    zfactor can be a variable (see below)
-  persp value = pfactor = amount of "perspective" in image
-    pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
-    pfactor can be a variable (see below)
-  box values = yes/no diam = draw outline of simulation box
-    yes/no = do or do not draw simulation box lines
-    diam = diameter of box lines as fraction of shortest box length
-  axes values = yes/no length diam = draw xyz axes
-    yes/no = do or do not draw xyz axes lines next to simulation box
-    length = length of axes lines as fraction of respective box lengths
-    diam = diameter of axes lines as fraction of shortest box length
-  subbox values = yes/no diam = draw outline of processor sub-domains
-    yes/no = do or do not draw sub-domain lines
-    diam = diameter of sub-domain lines as fraction of shortest box length
-  shiny value = sfactor = shinyness of spheres and cylinders
-    sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
-  ssao value = yes/no seed dfactor = SSAO depth shading
-    yes/no = turn depth shading on/off
-    seed = random # seed (positive integer)
-    dfactor = strength of shading from 0.0 to 1.0 
-
      - -
    -

    Examples: -

    -
    dump d0 all image 100 dump.*.jpg type type
-dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
-dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
-dump m0 all movie 1000 movie.mpg type type size 640 480
-dump m1 all movie 1000 movie.avi type type size 640 480
-dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720 
-
    -

    Description: -

    -

    Dump a high-quality rendered image of the atom configuration every N -timesteps and save the images either as a sequence of JPEG or PNG or -PPM files, or as a single movie file. The options for this command as -well as the dump_modify command control what is -included in the image or movie and how it appears. A series of such -images can easily be manually converted into an animated movie of your -simulation or the process can be automated without writing the -intermediate files using the dump movie style; see further details -below. Other dump styles store snapshots of numerical data asociated -with atoms in various formats, as discussed on the dump -doc page. -

    -

    Note that a set of images or a movie can be made after a simulation -has been run, using the rerun command to read snapshots -from an existing dump file, and using these dump commands in the rerun -script to generate the images/movie. -

    -

    Here are two sample images, rendered as 1024x1024 JPEG files. Click -to see the full-size images: -

    -
    - - - - - -
    - -

    Only atoms in the specified group are rendered in the image. The -dump_modify region and thresh commands can also -alter what atoms are included in the image.

    -

    The filename suffix determines whether a JPEG, PNG, or PPM file is -created with the image dump style. If the suffix is ".jpg" or -".jpeg", then a JPEG format file is created, if the suffix is ".png", -then a PNG format is created, else a PPM (aka NETPBM) format file is -created. The JPEG and PNG files are binary; PPM has a text mode -header followed by binary data. JPEG images have lossy compression; -PNG has lossless compression; and PPM files are uncompressed but can -be compressed with gzip, if LAMMPS has been compiled with --DLAMMPS_GZIP and a ".gz" suffix is used. -

    -

    Similarly, the format of the resulting movie is chosen with the -movie dump style. This is handled by the underlying FFmpeg converter -and thus details have to be looked up in the FFmpeg documentation. -Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif -Additional settings of the movie compression like bitrate and -framerate can be set using the dump_modify command. -

    -

    To write out JPEG and PNG format files, you must build LAMMPS with -support for the corresponding JPEG or PNG library. To convert images -into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG -flag. See this section of the manual -for instructions on how to do this. -

    -

    IMPORTANT NOTE: Because periodic boundary conditions are enforced only -on timesteps when neighbor lists are rebuilt, the coordinates of an -atom in the image may be slightly outside the simulation box. -

    -
    - -

    Dumps are performed on timesteps that are a multiple of N (including -timestep 0) and on the last timestep of a minimization if the -minimization converges. Note that this means a dump will not be -performed on the initial timestep after the dump command is invoked, -if the current timestep is not a multiple of N. This behavior can be -changed via the dump_modify first command, which -can be useful if the dump command is invoked after a minimization -ended on an arbitrary timestep. N can be changed between runs by -using the dump_modify every command. -

    -

    Dump image filenames must contain a wildcard character "*", so that -one image file per snapshot is written. The "*" character is replaced -with the timestep value. For example, tmp.dump.*.jpg becomes -tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note -that the dump_modify pad command can be used to -insure all timestep numbers are the same length (e.g. 00010), which -can make it easier to convert a series of images into a movie in the -correct ordering. -

    -

    Dump movie filenames on the other hand, must not have any wildcard -character since only one file combining all images into a single -movie will be written by the movie encoder. -

    -
    - -

    The color and diameter settings determine the color and size of -atoms rendered in the image. They can be any atom attribute defined -for the dump custom command, including type and -element. This includes per-atom quantities calculated by a -compute, fix, or variable, -which are prefixed by "c_", "f_", or "v_" respectively. Note that the -diameter setting can be overridden with a numeric value by the -optional adiam keyword, in which case you can specify the diameter -setting with any valid atom attribute. -

    -

    If type is specified for the color setting, then the color of each -atom is determined by its atom type. By default the mapping of types -to colors is as follows: -

    -
    • type 1 = red -
    • type 2 = green -
    • type 3 = blue -
    • type 4 = yellow -
    • type 5 = aqua -
    • type 6 = cyan -
    -

    and repeats itself for types > 6. This mapping can be changed by the -dump_modify acolor command. -

    -

    If type is specified for the diameter setting then the diameter of -each atom is determined by its atom type. By default all types have -diameter 1.0. This mapping can be changed by the dump_modify -adiam command. -

    -

    If element is specified for the color and/or diameter setting, -then the color and/or diameter of each atom is determined by which -element it is, which in turn is specified by the element-to-type -mapping specified by the "dump_modify element" command. By default -every atom type is C (carbon). Every element has a color and diameter -associated with it, which is the same as the colors and sizes used by -the AtomEye visualization package. -

    - - -

    If other atom attributes are used for the color or diameter -settings, they are interpreted in the following way. -

    -

    If "vx", for example, is used as the color setting, then the color -of the atom will depend on the x-component of its velocity. The -association of a per-atom value with a specific color is determined by -a "color map", which can be specified via the -dump_modify command. The basic idea is that the -atom-attribute will be within a range of values, and every value -within the range is mapped to a specific color. Depending on how the -color map is defined, that mapping can take place via interpolation so -that a value of -3.2 is halfway between "red" and "blue", or -discretely so that the value of -3.2 is "orange". -

    -

    If "vx", for example, is used as the diameter setting, then the atom -will be rendered using the x-component of its velocity as the -diameter. If the per-atom value <= 0.0, them the atom will not be -drawn. Note that finite-size spherical particles, as defined by -atom_style sphere define a per-particle radius or -diameter, which can be used as the diameter setting. -

    -
    - -

    The various kewords listed above control how the image is rendered. -As listed below, all of the keywords have defaults, most of which you -will likely not need to change. The dump modify -also has options specific to the dump image style, particularly for -assigning colors to atoms, bonds, and other image features. -

    -
    - -

    The adiam keyword allows you to override the diameter setting to a -per-atom attribute with a specified numeric value. All atoms will be -drawn with that diameter, e.g. 1.5, which is in whatever distance -units the input script defines, e.g. Angstroms. -

    -

    The atom keyword allow you to turn off the drawing of all atoms, -if the specified value is no. -

    -

    The bond keyword allows to you to alter how bonds are drawn. A bond -is only drawn if both atoms in the bond are being drawn due to being -in the specified group and due to other selection criteria -(e.g. region, threshhold settings of the -dump_modify command). By default, bonds are drawn -if they are defined in the input data file as read by the -read_data command. Using none for both the bond -color and width value will turn off the drawing of all bonds. -

    -

    If atom is specified for the bond color value, then each bond is -drawn in 2 halves, with the color of each half being the color of the -atom at that end of the bond. -

    -

    If type is specified for the color value, then the color of each -bond is determined by its bond type. By default the mapping of bond -types to colors is as follows: -

    -
    • type 1 = red -
    • type 2 = green -
    • type 3 = blue -
    • type 4 = yellow -
    • type 5 = aqua -
    • type 6 = cyan -
    -

    and repeats itself for bond types > 6. This mapping can be changed by -the dump_modify bcolor command. -

    -

    The bond width value can be a numeric value or atom or type (or -none as indicated above). -

    -

    If a numeric value is specified, then all bonds will be drawn as -cylinders with that diameter, e.g. 1.0, which is in whatever distance -units the input script defines, e.g. Angstroms. -

    -

    If atom is specified for the width value, then each bond -will be drawn with a width corresponding to the minimum diameter -of the 2 atoms in the bond. -

    -

    If type is specified for the width value then the diameter of each -bond is determined by its bond type. By default all types have -diameter 0.5. This mapping can be changed by the dump_modify -bdiam command. -

    -
    - -

    The size keyword sets the width and height of the created images, -i.e. the number of pixels in each direction. -

    -
    - -

    The view, center, up, zoom, and persp values determine how -3d simulation space is mapped to the 2d plane of the image. Basically -they control how the simulation box appears in the image. -

    -

    All of the view, center, up, zoom, and persp values can be -specified as numeric quantities, whose meaning is explained below. -Any of them can also be specified as an equal-style -variable, by using v_name as the value, where "name" is -the variable name. In this case the variable will be evaluated on the -timestep each image is created to create a new value. If the -equal-style variable is time-dependent, this is a means of changing -the way the simulation box appears from image to image, effectively -doing a pan or fly-by view of your simulation. -

    -

    The view keyword determines the viewpoint from which the simulation -box is viewed, looking towards the center point. The theta value -is the vertical angle from the +z axis, and must be an angle from 0 to -180 degrees. The phi value is an azimuthal angle around the z axis -and can be positive or negative. A value of 0.0 is a view along the -+x axis, towards the center point. If theta or phi are -specified via variables, then the variable values should be in -degrees. -

    -

    The center keyword determines the point in simulation space that -will be at the center of the image. Cx, Cy, and Cz are -speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is -the center of the simulation box. These values do not have to be -between 0.0 and 1.0, if you want the simulation box to be offset from -the center of the image. Note, however, that if you choose strange -values for Cx, Cy, or Cz you may get a blank image. Internally, -Cx, Cy, and Cz are converted into a point in simulation space. -If flag is set to "s" for static, then this conversion is done once, -at the time the dump command is issued. If flag is set to "d" for -dynamic then the conversion is performed every time a new image is -created. If the box size or shape is changing, this will adjust the -center point in simulation space. -

    -

    The up keyword determines what direction in simulation space will be -"up" in the image. Internally it is stored as a vector that is in the -plane perpendicular to the view vector implied by the theta and -pni values, and which is also in the plane defined by the view -vector and user-specified up vector. Thus this internal vector is -computed from the user-specified up vector as -

    -
    up_internal = view cross (up cross view) 
-
    -

    This means the only restriction on the specified up vector is that -it cannot be parallel to the view vector, implied by the theta and -phi values. -

    -

    The zoom keyword scales the size of the simulation box as it appears -in the image. The default zfactor value of 1 should display an -image mostly filled by the atoms in the simulation box. A zfactor > -1 will make the simulation box larger; a zfactor < 1 will make it -smaller. Zfactor must be a value > 0.0. -

    -

    The persp keyword determines how much depth perspective is present -in the image. Depth perspective makes lines that are parallel in -simulation space appear non-parallel in the image. A pfactor value -of 0.0 means that parallel lines will meet at infininty (1.0/pfactor), -which is an orthographic rendering with no persepctive. A pfactor -value between 0.0 and 1.0 will introduce more perspective. A pfactor -value > 1 will create a highly skewed image with a large amount of -perspective. -

    -

    IMPORTANT NOTE: The persp keyword is not yet supported as an option. -

    -
    - -

    The box keyword determines if and how the simulation box boundaries -are rendered as thin cylinders in the image. If no is set, then the -box boundaries are not drawn and the diam setting is ignored. If -yes is set, the 12 edges of the box are drawn, with a diameter that -is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for -2d). The color of the box boundaries can be set with the dump_modify -boxcolor command. -

    -

    The axes keyword determines if and how the coordinate axes are -rendered as thin cylinders in the image. If no is set, then the -axes are not drawn and the length and diam settings are ignored. -If yes is set, 3 thin cylinders are drawn to represent the x,y,z -axes in colors red,green,blue. The origin of these cylinders will be -offset from the lower left corner of the box by 10%. The length -setting determines how long the cylinders will be as a fraction of the -respective box lengths. The diam setting determines their thickness -as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for -2d). -

    -

    The subbox keyword determines if and how processor sub-domain -boundaries are rendered as thin cylinders in the image. If no is -set (default), then the sub-domain boundaries are not drawn and the -diam setting is ignored. If yes is set, the 12 edges of each -processor sub-domain are drawn, with a diameter that is a fraction of -the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color -of the sub-domain boundaries can be set with the dump_modify -boxcolor command. -

    -
    - -

    The shiny keyword determines how shiny the objects rendered in the -image will appear. The sfactor value must be a value 0.0 <= -sfactor <= 1.0, where sfactor = 1 is a highly reflective surface -and sfactor = 0 is a rough non-shiny surface. -

    -

    The ssao keyword turns on/off a screen space ambient occlusion -(SSAO) model for depth shading. If yes is set, then atoms further -away from the viewer are darkened via a randomized process, which is -perceived as depth. The calculation of this effect can increase the -cost of computing the image by roughly 2x. The strength of the effect -can be scaled by the dfactor parameter. If no is set, no depth -shading is performed. -

    -
    - -

    A series of JPEG, PNG, or PPM images can be converted into a movie -file and then played as a movie using commonly available tools. Using -dump style movie automates this step and avoids the intermediate -step of writing (many) image snapshot file. But LAMMPS has to be -compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be -installed. -

    -

    To manually convert JPEG, PNG or PPM files into an animated GIF or -MPEG or other movie file you can use: -

    -
    • a) Use the ImageMagick convert program. - -
      % convert *.jpg foo.gif
-% convert -loop 1 *.ppm foo.mpg 
-
      -

      Animated GIF files from ImageMagick are unoptimized. You can use a -program like gifsicle to optimize and massively shrink them. -MPEG files created by ImageMagick are in MPEG-1 format with rather -inefficient compression and low quality. -

      -
    • b) Use QuickTime. - -

      Select "Open Image Sequence" under the File menu Load the images into -QuickTime to animate them Select "Export" under the File menu Save the -movie as a QuickTime movie (*.mov) or in another format. QuickTime -can generate very high quality and efficiently compressed movie -files. Some of the supported formats require to buy a license and some -are not readable on all platforms until specific runtime libraries are -installed. -

      -
    • c) Use FFmpeg - -

      FFmpeg is a command line tool that is available on many platforms and -allows extremely flexible encoding and decoding of movies. -

      -
      cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
-cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi 
-
      -

      Frontends for FFmpeg exist for multiple platforms. For more -information see the FFmpeg homepage -

      - -
    -
    - -

    Play the movie: -

    -
    • a) Use your browser to view an animated GIF movie. - -

      Select "Open File" under the File menu -Load the animated GIF file -

      -
    • b) Use the freely available mplayer or ffplay tool to view a -movie. Both are available for multiple OSes and support a large -variety of file formats and decoders. - -
      % mplayer foo.mpg 
-% ffplay bar.avi 
-
      -
    • c) Use the Pizza.py -animate tool, -which works directly on a series of image files. - -
      a = animate("foo*.jpg") 
-
      -
    • d) QuickTime and other Windows- or MacOS-based media players can -obviously play movie files directly. Similarly for corresponding tools -bundled with Linux desktop environments. However, due to licensing -issues with some file formats, the formats may require installing -additional libraries, purchasing a license, or may not be -supported. -
    -
    - -

    See Section_modify of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. -

    -
    - -

    Restrictions: -

    -

    To write JPEG images, you must use the -DLAMMPS_JPEG switch when -building LAMMPS and link with a JPEG library. To write PNG images, you -must use the -DLAMMPS_PNG switch when building LAMMPS and link with a -PNG library. -

    -

    To write movie dumps, you must use the -DLAMMPS_FFMPEG switch when -building LAMMPS and have the FFmpeg executable available on the -machine where LAMMPS is being run. Typically it's name is lowercase, -i.e. ffmpeg. -

    -

    See the Making LAMMPS section of the -documentation for details on how to compile with optional switches. -

    -

    Note that since FFmpeg is run as an external program via a pipe, -LAMMPS has limited control over its execution and no knowledge about -errors and warnings printed by it. Those warnings and error messages -will be printed to the screen only. Due to the way image data is -communicated to FFmpeg, it will often print the message -

    -
    pipe:: Input/output error 
-
    -

    which can be safely ignored. Other warnings -and errors have to be addressed according to the FFmpeg documentation. -One known issue is that certain movie file formats (e.g. MPEG level 1 -and 2 format streams) have video bandwith limits that can be crossed -when rendering too large of image sizes. Typical warnings look like -this: -

    -
    [mpeg @ 0x98b5e0] packet too large, ignoring buffer limits to mux it
-[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
-[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018 
-
    -

    In this case it is recommended to either reduce the size of the image -or encode in a different format that is also supported by your copy of -FFmpeg, and which does not have this limitation (e.g. .avi, .mkv, -mp4). -

    -

    Related commands: -

    -

    dump, dump_modify, undump -

    -

    Default: -

    -

    The defaults for the keywords are as follows: -

    -
    • adiam = not specified (use diameter setting) -
    • atom = yes -
    • bond = none none (if no bonds in system) -
    • bond = atom 0.5 (if bonds in system) -
    • size = 512 512 -
    • view = 60 30 (for 3d) -
    • view = 0 0 (for 2d) -
    • center = s 0.5 0.5 0.5 -
    • up = 0 0 1 (for 3d) -
    • up = 0 1 0 (for 2d) -
    • zoom = 1.0 -
    • persp = 0.0 -
    • box = yes 0.02 -
    • axes = no 0.0 0.0 -
    • subbox no 0.0 -
    • shiny = 1.0 -
    • ssao = no -
    - diff --git a/doc/doc2/dump_modify.html b/doc/doc2/dump_modify.html deleted file mode 100644 index 10d5592c30..0000000000 --- a/doc/doc2/dump_modify.html +++ /dev/null @@ -1,817 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dump_modify command -

    -

    Syntax: -

    -
    dump_modify dump-ID keyword values ... 
-
    -
    • dump-ID = ID of dump to modify - -
    • one or more keyword/value pairs may be appended - -
    • these keywords apply to various dump styles - -
    • keyword = append or buffer or element or every or fileper or first or flush or format or image or label or nfile or pad or precision or region or scale or sort or thresh or unwrap - -
        append arg = yes or no
-  buffer arg = yes or no
-  element args = E1 E2 ... EN, where N = # of atom types
-    E1,...,EN = element name, e.g. C or Fe or Ga
-  every arg = N
-    N = dump every this many timesteps
-    N can be a variable (see below)
-  fileper arg = Np
-    Np = write one file for every this many processors
-  first arg = yes or no
-  format arg = C-style format string for one line of output
-  flush arg = yes or no
-  image arg = yes or no
-  label arg = string
-    string = character string (e.g. BONDS) to use in header of dump local file
-  nfile arg = Nf
-    Nf = write this many files, one from each of Nf processors
-  pad arg = Nchar = # of characters to convert timestep to
-  precision arg = power-of-10 value from 10 to 1000000
-  region arg = region-ID or "none"
-  scale arg = yes or no
-  sfactor arg = coordinate scaling factor (> 0.0)
-  tfactor arg = time scaling factor (> 0.0)
-  sort arg = off or id or N or -N
-     off = no sorting of per-atom lines within a snapshot
-     id = sort per-atom lines by atom ID
-     N = sort per-atom lines in ascending order by the Nth column
-     -N = sort per-atom lines in descending order by the Nth column
-  thresh args = attribute operation value
-    attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
-    operation = "<" or "<=" or ">" or ">=" or "==" or "!="
-    value = numeric value to compare to
-    these 3 args can be replaced by the word "none" to turn off thresholding
-  unwrap arg = yes or no 
-
      -
    • these keywords apply only to the image and movie styles - -
    • keyword = acolor or adiam or amap or backcolor or bcolor or bdiam or boxcolor or color or bitrate or framerate - -
        acolor args = type color
-    type = atom type or range of types (see below)
-    color = name of color or color1/color2/...
-  adiam args = type diam
-    type = atom type or range of types (see below)
-    diam = diameter of atoms of that type (distance units)
-  amap args = lo hi style delta N entry1 entry2 ... entryN
-    lo = number or min = lower bound of range of color map
-    hi = number or max = upper bound of range of color map
-    style = 2 letters = "c" or "d" or "s" plus "a" or "f"
-      "c" for continuous
-      "d" for discrete
-      "s" for sequential
-      "a" for absolute
-      "f" for fractional
-    delta = binsize (only used for style "s", otherwise ignored)
-      binsize = range is divided into bins of this width
-    N = # of subsequent entries
-    entry = value color (for continuous style)
-      value = number or min or max = single value within range
-      color = name of color used for that value
-    entry = lo hi color (for discrete style)
-      lo/hi = number or min or max = lower/upper bound of subset of range
-      color = name of color used for that subset of values
-    entry = color (for sequential style)
-      color = name of color used for a bin of values
-  backcolor arg = color
-    color = name of color for background
-  bcolor args = type color
-    type = bond type or range of types (see below)
-    color = name of color or color1/color2/...
-  bdiam args = type diam
-    type = bond type or range of types (see below)
-    diam = diameter of bonds of that type (distance units)
-  boxcolor arg = color
-    color = name of color for simulation box lines and processor sub-domain lines
-  color args = name R G B
-    name = name of color
-    R,G,B = red/green/blue numeric values from 0.0 to 1.0
-  bitrate arg = rate
-    rate = target bitrate for movie in kbps
-  framerate arg = fps
-    fps = frames per second for movie 
-
      - -
    -

    Examples: -

    -
    dump_modify 1 format "%d %d %20.15g %g %g" scale yes
-dump_modify myDump image yes scale no flush yes
-dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
-dump_modify xtcdump precision 10000 sfactor 0.1
-dump_modify 1 every 1000 nfile 20
-dump_modify 1 every v_myVar
-dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red 
-
    -

    Description: -

    -

    Modify the parameters of a previously defined dump command. Not all -parameters are relevant to all dump styles. -

    -

    As explained on the dump doc page, the atom/mpiio, -custom/mpiio, and xyz/mpiio dump styles are identical in command -syntax and in the format of the dump files they create, to the -corresponding styles without "mpiio", except the single dump file they -produce is written in parallel via the MPI-IO library. Thus if a -dump_modify option below is valid for the atom style, it is also -valid for the atom/mpiio style, and similarly for the other styles -which allow for use of MPI-IO. -

    -
    - -
    - -

    These keywords apply to various dump styles, including the dump -image and dump movie styles. The -description gives details. -

    -
    - -

    The append keyword applies to all dump styles except cfg and xtc -and dcd. It also applies only to text output files, not to binary -or gzipped or image/movie files. If specified as yes, then dump -snapshots are appended to the end of an existing dump file. If -specified as no, then a new dump file will be created which will -overwrite an existing file with the same name. This keyword can only -take effect if the dump_modify command is used after the -dump command, but before the first command that causes -dump snapshots to be output, e.g. a run or -minimize command. Once the dump file has been opened, -this keyword has no further effect. -

    -
    - -

    The buffer keyword applies only to dump styles atom, cfg, -custom, local, and xyz. It also applies only to text output -files, not to binary or gzipped files. If specified as yes, which -is the default, then each processor writes its output into an internal -text buffer, which is then sent to the processor(s) which perform file -writes, and written by those processors(s) as one large chunk of text. -If specified as no, each processor sends its per-atom data in binary -format to the processor(s) which perform file wirtes, and those -processor(s) format and write it line by line into the output file. -

    -

    The buffering mode is typically faster since each processor does the -relatively expensive task of formatting the output for its own atoms. -However it requires about twice the memory (per processor) for the -extra buffering. -

    -
    - -

    The element keyword applies only to the the dump cfg, xyz, and -image styles. It associates element names (e.g. H, C, Fe) with -LAMMPS atom types. See the list of element names at the bottom of -this page. -

    -

    In the case of dump cfg, this allows the AtomEye -visualization package to read the dump file and render atoms with the -appropriate size and color. -

    -

    In the case of dump image, the output images will follow the same -AtomEye convention. An element name is specified for each -atom type (1 to Ntype) in the simulation. The same element name can -be given to multiple atom types. -

    -

    In the case of xyz format dumps, there are no restrictions to what -label can be used as an element name. Any whitespace separated text -will be accepted. -

    - - -
    - -

    The every keyword changes the dump frequency originally specified by -the dump command to a new value. The every keyword can be -specified in one of two ways. It can be a numeric value in which case -it must be > 0. Or it can be an equal-style variable, -which should be specified as v_name, where name is the variable name. -

    -

    In this case, the variable is evaluated at the beginning of a run to -determine the next timestep at which a dump snapshot will be written -out. On that timestep the variable will be evaluated again to -determine the next timestep, etc. Thus the variable should return -timestep values. See the stagger() and logfreq() and stride() math -functions for equal-style variables, as examples of -useful functions to use in this context. Other similar math functions -could easily be added as options for equal-style -variables. Also see the next() function, which allows -use of a file-style variable which reads successive values from a -file, each time the variable is evaluated. Used with the every -keyword, if the file contains a list of ascending timesteps, you can -output snapshots whenever you wish. -

    -

    Note that when using the variable option with the every keyword, you -need to use the first option if you want an initial snapshot written -to the dump file. The every keyword cannot be used with the dump -dcd style. -

    -

    For example, the following commands will -write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc: -

    -
    variable	s equal logfreq(10,3,10)
-dump		1 all atom 100 tmp.dump
-dump_modify	1 every v_s first yes 
-
    -

    The following commands would write snapshots at the timesteps listed -in file tmp.times: -

    -
    variable        f file tmp.times
-variable	s equal next(f)
-dump		1 all atom 100 tmp.dump
-dump_modify	1 every v_s 
-
    -

    IMPORTANT NOTE: When using a file-style variable with the every -keyword, the file of timesteps must list a first timestep that is -beyond the current timestep (e.g. it cannot be 0). And it must list -one or more timesteps beyond the length of the run you perform. This -is because the dump command will generate an error if the next -timestep it reads from the file is not a value greater than the -current timestep. Thus if you wanted output on steps 0,15,100 of a -100-timestep run, the file should contain the values 15,100,101 and -you should also use the dump_modify first command. Any final value > -100 could be used in place of 101. -

    -
    - -

    The first keyword determines whether a dump snapshot is written on -the very first timestep after the dump command is invoked. This will -always occur if the current timestep is a multiple of N, the frequency -specified in the dump command, including timestep 0. But -if this is not the case, a dump snapshot will only be written if the -setting of this keyword is yes. If it is no, which is the -default, then it will not be written. -

    -
    - -

    The flush keyword determines whether a flush operation is invoked -after a dump snapshot is written to the dump file. A flush insures -the output in that file is current (no buffering by the OS), even if -LAMMPS halts before the simulation completes. Flushes cannot be -performed with dump style xtc. -

    -
    - -

    The text-based dump styles have a default C-style format string which -simply specifies %d for integers and %g for floating-point values. -The format keyword can be used to override the default with a new -C-style format string. Do not include a trailing "\\n" newline -character in the format string. This option has no effect on the -dcd and xtc dump styles since they write binary files. Note that -for the cfg style, the first two fields (atom id and type) are not -actually written into the CFG file, though you must include formats -for them in the format string. -

    -

    IMPORTANT NOTE: Any value written to a text-based dump file that is a -per-atom quantity calculated by a compute or -fix is stored internally as a floating-point value. If the -value is actually an integer and you wish it to appear in the text -dump file as a (large) integer, then you need to use an appropriate -format. For example, these commands: -

    -
    compute     1 all property/local batom1 batom2
-dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
-dump_modify 1 format "%d %0.0f %0.0f" 
-
    -

    will output the two atom IDs for atoms in each bond as integers. If -the dump_modify command were omitted, they would appear as -floating-point values, assuming they were large integers (more than 6 -digits). The "index" keyword should use the "%d" format since it is -not generated by a compute or fix, and is stored internally as an -integer. -

    -
    - -

    The fileper keyword is documented below with the nfile keyword. -

    -
    - -

    The image keyword applies only to the dump atom style. If the -image value is yes, 3 flags are appended to each atom's coords which -are the absolute box image of the atom in each dimension. For -example, an x image flag of -2 with a normalized coord of 0.5 means -the atom is in the center of the box, but has passed thru the box -boundary 2 times and is really 2 box lengths to the left of its -current coordinate. Note that for dump style custom these various -values can be printed in the dump file by using the appropriate atom -attributes in the dump command itself. -

    -
    - -

    The label keyword applies only to the dump local style. When -it writes local information, such as bond or angle topology -to a dump file, it will use the specified label to format -the header. By default this includes 2 lines: -

    -
    ITEM: NUMBER OF ENTRIES
-ITEM: ENTRIES ... 
-
    -

    The word "ENTRIES" will be replaced with the string specified, -e.g. BONDS or ANGLES. -

    -
    - -

    The nfile or fileper keywords can be used in conjunction with the -"%" wildcard character in the specified dump file name, for all dump -styles except the dcd, image, movie, xtc, and xyz styles -(for which "%" is not allowed). As explained on the dump -command doc page, the "%" character causes the dump file to be written -in pieces, one piece for each of P processors. By default P = the -number of processors the simulation is running on. The nfile or -fileper keyword can be used to set P to a smaller value, which can -be more efficient when running on a large number of processors. -

    -

    The nfile keyword sets P to the specified Nf value. For example, if -Nf = 4, and the simulation is running on 100 processors, 4 files will -be written, by processors 0,25,50,75. Each will collect information -from itself and the next 24 processors and write it to a dump file. -

    -

    For the fileper keyword, the specified value of Np means write one -file for every Np processors. For example, if Np = 4, every 4th -processor (0,4,8,12,etc) will collect information from itself and the -next 3 processors and write it to a dump file. -

    -
    - -

    The pad keyword only applies when the dump filename is specified -with a wildcard "*" character which becomes the timestep. If pad is -0, which is the default, the timestep is converted into a string of -unpadded length, e.g. 100 or 12000 or 2000000. When pad is -specified with Nchar > 0, the string is padded with leading zeroes -so they are all the same length = Nchar. For example, pad 7 would -yield 0000100, 0012000, 2000000. This can be useful so that -post-processing programs can easily read the files in ascending -timestep order. -

    -
    - -

    The precision keyword only applies to the dump xtc style. A -specified value of N means that coordinates are stored to 1/N -nanometer accuracy, e.g. for N = 1000, the coordinates are written to -1/1000 nanometer accuracy. -

    -
    - -

    The sfactor and tfactor keywords only apply to the dump xtc -style. They allow customization of the unit conversion factors used -when writing to XTC files. By default they are initialized for -whatever units style is being used, to write out -coordinates in nanometers and time in picoseconds. I.e. for real -units, LAMMPS defines sfactor = 0.1 and tfactor = 0.001, since the -Angstroms and fmsec used by real units are 0.1 nm and 0.001 psec -respectively. If you are using a units system with distance and time -units far from nm and psec, you may wish to write XTC files with -different units, since the compression algorithm used in XTC files is -most effective when the typical magnitude of position data is between -10.0 and 0.1. -

    -
    - -

    The region keyword only applies to the dump custom, cfg, -image, and movie styles. If specified, only atoms in the region -will be written to the dump file or included in the image/movie. Only -one region can be applied as a filter (the last one specified). See -the region command for more details. Note that a region -can be defined as the "inside" or "outside" of a geometric shape, and -it can be the "union" or "intersection" of a series of simpler -regions. -

    -
    - -

    The scale keyword applies only to the dump atom style. A scale -value of yes means atom coords are written in normalized units from -0.0 to 1.0 in each box dimension. If the simluation box is triclinic -(tilted), then all atom coords will still be between 0.0 and 1.0. A -value of no means they are written in absolute distance units -(e.g. Angstroms or sigma). -

    -
    - -

    The sort keyword determines whether lines of per-atom output in a -snapshot are sorted or not. A sort value of off means they will -typically be written in indeterminate order, either in serial or -parallel. This is the case even in serial if the atom_modify -sort option is turned on, which it is by default, to -improve performance. A sort value of id means sort the output by -atom ID. A sort value of N or -N means sort the output by the value -in the Nth column of per-atom info in either ascending or descending -order. -

    -

    The dump local style cannot be sorted by atom ID, since there are -typically multiple lines of output per atom. Some dump styles, such -as dcd and xtc, require sorting by atom ID to format the output -file correctly. If multiple processors are writing the dump file, via -the "%" wildcard in the dump filename, then sorting cannot be -performed. -

    -

    IMPORTANT NOTE: Unless it is required by the dump style, sorting dump -file output requires extra overhead in terms of CPU and communication -cost, as well as memory, versus unsorted output. -

    -
    - -

    The thresh keyword only applies to the dump custom, cfg, -image, and movie styles. Multiple thresholds can be specified. -Specifying "none" turns off all threshold criteria. If thresholds are -specified, only atoms whose attributes meet all the threshold criteria -are written to the dump file or included in the image. The possible -attributes that can be tested for are the same as those that can be -specified in the dump custom command, with the exception -of the element attribute, since it is not a numeric value. Note -that different attributes can be output by the dump custom command -than are used as threshold criteria by the dump_modify command. -E.g. you can output the coordinates and stress of atoms whose energy -is above some threshold. -

    -
    - -

    The unwrap keyword only applies to the dump dcd and xtc styles. -If set to yes, coordinates will be written "unwrapped" by the image -flags for each atom. Unwrapped means that if the atom has passed thru -a periodic boundary one or more times, the value is printed for what -the coordinate would be if it had not been wrapped back into the -periodic box. Note that these coordinates may thus be far outside the -box size stored with the snapshot. -

    -
    - -
    - -

    These keywords apply only to the dump image and -dump movie styles. Any keyword that affects an -image, also affects a movie, since the movie is simply a collection of -images. Some of the keywords only affect the dump -movie style. The descriptions give details. -

    -
    - -

    The acolor keyword can be used with the dump image -command, when its atom color setting is type, to set the color that -atoms of each type will be drawn in the image. -

    -

    The specified type should be an integer from 1 to Ntypes = the -number of atom types. A wildcard asterisk can be used in place of or -in conjunction with the type argument to specify a range of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). -

    -

    The specified color can be a single color which is any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. Or it can be two or more colors separated -by a "/" character, e.g. red/green/blue. In the former case, that -color is assigned to all the specified atom types. In the latter -case, the list of colors are assigned in a round-robin fashion to each -of the specified atom types. -

    -
    - -

    The adiam keyword can be used with the dump image -command, when its atom diameter setting is type, to set the size -that atoms of each type will be drawn in the image. The specified -type should be an integer from 1 to Ntypes. As with the acolor -keyword, a wildcard asterisk can be used as part of the type -argument to specify a range of atomt types. The specified diam is -the size in whatever distance units the input script is -using, e.g. Angstroms. -

    -
    - -

    The amap keyword can be used with the dump image -command, with its atom keyword, when its atom setting is an -atom-attribute, to setup a color map. The color map is used to assign -a specific RGB (red/green/blue) color value to an individual atom when -it is drawn, based on the atom's attribute, which is a numeric value, -e.g. its x-component of velocity if the atom-attribute "vx" was -specified. -

    -

    The basic idea of a color map is that the atom-attribute will be -within a range of values, and that range is associated with a a series -of colors (e.g. red, blue, green). An atom's specific value (vx = --3.2) can then mapped to the series of colors (e.g. halfway between -red and blue), and a specific color is determined via an interpolation -procedure. -

    -

    There are many possible options for the color map, enabled by the -amap keyword. Here are the details. -

    -

    The lo and hi settings determine the range of values allowed for -the atom attribute. If numeric values are used for lo and/or hi, -then values that are lower/higher than that value are set to the -value. I.e. the range is static. If lo is specified as min or -hi as max then the range is dynamic, and the lower and/or -upper bound will be calculated each time an image is drawn, based -on the set of atoms being visualized. -

    -

    The style setting is two letters, such as "ca". The first letter is -either "c" for continuous, "d" for discrete, or "s" for sequential. -The second letter is either "a" for absolute, or "f" for fractional. -

    -

    A continuous color map is one in which the color changes continuously -from value to value within the range. A discrete color map is one in -which discrete colors are assigned to sub-ranges of values within the -range. A sequential color map is one in which discrete colors are -assigned to a sequence of sub-ranges of values covering the entire -range. -

    -

    An absolute color map is one in which the values to which colors are -assigned are specified explicitly as values within the range. A -fractional color map is one in which the values to which colors are -assigned are specified as a fractional portion of the range. For -example if the range is from -10.0 to 10.0, and the color red is to be -assigned to atoms with a value of 5.0, then for an absolute color map -the number 5.0 would be used. But for a fractional map, the number -0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0. -

    -

    The delta setting must be specified for all styles, but is only used -for the sequential style; otherwise the value is ignored. It -specifies the bin size to use within the range for assigning -consecutive colors to. For example, if the range is from -10.0 to -10.0 and a delta of 1.0 is used, then 20 colors will be assigned to -the range. The first will be from -10.0 <= color1 < -9.0, then 2nd -from -9.0 <= color2 < -8.0, etc. -

    -

    The N setting is how many entries follow. The format of the entries -depends on whether the color map style is continuous, discrete or -sequential. In all cases the color setting can be any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. -

    -

    For continuous color maps, each entry has a value and a color. -The value is either a number within the range of values or min or -max. The value of the first entry must be min and the value -of the last entry must be max. Any entries in between must have -increasing values. Note that numeric values can be specified either -as absolute numbers or as fractions (0.0 to 1.0) of the range, -depending on the "a" or "f" in the style setting for the color map. -

    -

    Here is how the entries are used to determine the color of an -individual atom, given the value X of its atom attribute. X will fall -between 2 of the entry values. The color of the atom is linearly -interpolated (in each of the RGB values) between the 2 colors -associated with those entries. For example, if X = -5.0 and the 2 -surrounding entries are "red" at -10.0 and "blue" at 0.0, then the -atom's color will be halfway between "red" and "blue", which happens -to be "purple". -

    -

    For discrete color maps, each entry has a lo and hi value and a -color. The lo and hi settings are either numbers within the -range of values or lo can be min or hi can be max. The lo -and hi settings of the last entry must be min and max. Other -entries can have any lo and hi values and the sub-ranges of -different values can overlap. Note that numeric lo and hi values -can be specified either as absolute numbers or as fractions (0.0 to -1.0) of the range, depending on the "a" or "f" in the style setting -for the color map. -

    -

    Here is how the entries are used to determine the color of an -individual atom, given the value X of its atom attribute. The entries -are scanned from first to last. The first time that lo <= X <= -hi, X is assigned the color associated with that entry. You can -think of the last entry as assigning a default color (since it will -always be matched by X), and the earlier entries as colors that -override the default. Also note that no interpolation of a color RGB -is done. All atoms will be drawn with one of the colors in the list -of entries. -

    -

    For sequential color maps, each entry has only a color. Here is how -the entries are used to determine the color of an individual atom, -given the value X of its atom attribute. The range is partitioned -into N bins of width binsize. Thus X will fall in a specific bin -from 1 to N, say the Mth bin. If it falls on a boundary between 2 -bins, it is considered to be in the higher of the 2 bins. Each bin is -assigned a color from the E entries. If E < N, then the colors are -repeated. For example if 2 entries with colors red and green are -specified, then the odd numbered bins will be red and the even bins -green. The color of the atom is the color of its bin. Note that the -sequential color map is really a shorthand way of defining a discrete -color map without having to specify where all the bin boundaries are. -

    -

    Here is an example of using a sequential color map to color all the -atoms in individual molecules with a different color. See the -examples/pour/in.pour.2d.molecule input script for an example of how -this is used. -

    -
    variable        colors string &
-                "red green blue yellow white &
-                purple pink orange lime gray"
-variable	mol atom mol%10
-dump		1 all image 250 image.*.jpg v_mol type &
-		zoom 1.6 adiam 1.5
-dump_modify	1 pad 5 amap 0 10 sa 1 10 ${colors} 
-
    -

    In this case, 10 colors are defined, and molecule IDs are -mapped to one of the colors, even if there are 1000s of molecules. -

    -
    - -

    The backcolor sets the background color of the images. The color -name can be any of the 140 pre-defined colors (see below) or a color -name defined by the dump_modify color option. -

    -
    - -

    The bcolor keyword can be used with the dump image -command, with its bond keyword, when its color setting is type, to -set the color that bonds of each type will be drawn in the image. -

    -

    The specified type should be an integer from 1 to Nbondtypes = the -number of bond types. A wildcard asterisk can be used in place of or -in conjunction with the type argument to specify a range of bond -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of bond types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). -

    -

    The specified color can be a single color which is any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. Or it can be two or more colors separated -by a "/" character, e.g. red/green/blue. In the former case, that -color is assigned to all the specified bond types. In the latter -case, the list of colors are assigned in a round-robin fashion to each -of the specified bond types. -

    -
    - -

    The bdiam keyword can be used with the dump image -command, with its bond keyword, when its diam setting is type, to -set the diameter that bonds of each type will be drawn in the image. -The specified type should be an integer from 1 to Nbondtypes. As -with the bcolor keyword, a wildcard asterisk can be used as part of -the type argument to specify a range of bond types. The specified -diam is the size in whatever distance units you are -using, e.g. Angstroms. -

    -
    - -

    The bitrate keyword can be used with the dump -movie command to define the size of the resulting -movie file and its quality via setting how many kbits per second are -to be used for the movie file. Higher bitrates require less -compression and will result in higher quality movies. The quality is -also determined by the compression format and encoder. The default -setting is 2000 kbit/s, which will result in average quality with -older compression formats. -

    -

    IMPORTANT NOTE: Not all movie file formats supported by dump movie -allow the bitrate to be set. If not, the setting is silently ignored. -

    -
    - -

    The boxcolor keyword sets the color of the simulation box drawn -around the atoms in each image as well as the color of processor -sub-domain boundaries. See the "dump image box" command for how to -specify that a box be drawn via the box keyword, and the sub-domain -boundaries via the subbox keyword. The color name can be any of the -140 pre-defined colors (see below) or a color name defined by the -dump_modify color option. -

    -
    - -

    The color keyword allows definition of a new color name, in addition -to the 140-predefined colors (see below), and associates 3 -red/green/blue RGB values with that color name. The color name can -then be used with any other dump_modify keyword that takes a color -name as a value. The RGB values should each be floating point values -between 0.0 and 1.0 inclusive. -

    -

    When a color name is converted to RGB values, the user-defined color -names are searched first, then the 140 pre-defined color names. This -means you can also use the color keyword to overwrite one of the -pre-defined color names with new RBG values. -

    -
    - -

    The framerate keyword can be used with the dump -movie command to define the duration of the resulting -movie file. Movie files written by the dump movie command have a -default frame rate of 24 frames per second and the images generated -will be converted at that rate. Thus a sequence of 1000 dump images -will result in a movie of about 42 seconds. To make a movie run -longer you can either generate images more frequently or lower the -frame rate. To speed a movie up, you can do the inverse. Using a -frame rate higher than 24 is not recommended, as it will result in -simply dropping the rendered images. It is more efficient to dump -images less frequently. -

    -
    - -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    dump, dump image, undump -

    -

    Default: -

    -

    The option defaults are -

    -
    • append = no -
    • buffer = yes for dump styles atom, custom, loca, and xyz -
    • element = "C" for every atom type -
    • every = whatever it was set to via the dump command -
    • fileper = # of processors -
    • first = no -
    • flush = yes -
    • format = %d and %g for each integer or floating point value -
    • image = no -
    • label = ENTRIES -
    • nfile = 1 -
    • pad = 0 -
    • precision = 1000 -
    • region = none -
    • scale = yes -
    • sort = off for dump styles atom, custom, cfg, and local -
    • sort = id for dump styles dcd, xtc, and xyz -
    • thresh = none -
    • unwrap = no -
    -
    • acolor = * red/green/blue/yellow/aqua/cyan -
    • adiam = * 1.0 -
    • amap = min max cf 0.0 2 min blue max red -
    • backcolor = black -
    • bcolor = * red/green/blue/yellow/aqua/cyan -
    • bdiam = * 0.5 -
    • bitrate = 2000 -
    • boxcolor = yellow -
    • color = 140 color names are pre-defined as listed below -
    • framerate = 24 -
    -
    - -

    These are the standard 109 element names that LAMMPS pre-defines for -use with the dump image and dump_modify commands. -

    -
    • 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne" -
    • 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca" -
    • 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn" -
    • 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr" -
    • 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn" -
    • 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd" -
    • 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb" -
    • 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg" -
    • 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th" -
    • 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm" -
    • 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt" -
    -
    - -

    These are the 140 colors that LAMMPS pre-defines for use with the -dump image and dump_modify commands. Additional -colors can be defined with the dump_modify color command. The 3 -numbers listed for each name are the RGB (red/green/blue) values. -Divide each value by 255 to get the equivalent 0.0 to 1.0 value. -

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    aliceblue = 240, 248, 255 antiquewhite = 250, 235, 215 aqua = 0, 255, 255 aquamarine = 127, 255, 212 azure = 240, 255, 255
    beige = 245, 245, 220 bisque = 255, 228, 196 black = 0, 0, 0 blanchedalmond = 255, 255, 205 blue = 0, 0, 255
    blueviolet = 138, 43, 226 brown = 165, 42, 42 burlywood = 222, 184, 135 cadetblue = 95, 158, 160 chartreuse = 127, 255, 0
    chocolate = 210, 105, 30 coral = 255, 127, 80 cornflowerblue = 100, 149, 237 cornsilk = 255, 248, 220 crimson = 220, 20, 60
    cyan = 0, 255, 255 darkblue = 0, 0, 139 darkcyan = 0, 139, 139 darkgoldenrod = 184, 134, 11 darkgray = 169, 169, 169
    darkgreen = 0, 100, 0 darkkhaki = 189, 183, 107 darkmagenta = 139, 0, 139 darkolivegreen = 85, 107, 47 darkorange = 255, 140, 0
    darkorchid = 153, 50, 204 darkred = 139, 0, 0 darksalmon = 233, 150, 122 darkseagreen = 143, 188, 143 darkslateblue = 72, 61, 139
    darkslategray = 47, 79, 79 darkturquoise = 0, 206, 209 darkviolet = 148, 0, 211 deeppink = 255, 20, 147 deepskyblue = 0, 191, 255
    dimgray = 105, 105, 105 dodgerblue = 30, 144, 255 firebrick = 178, 34, 34 floralwhite = 255, 250, 240 forestgreen = 34, 139, 34
    fuchsia = 255, 0, 255 gainsboro = 220, 220, 220 ghostwhite = 248, 248, 255 gold = 255, 215, 0 goldenrod = 218, 165, 32
    gray = 128, 128, 128 green = 0, 128, 0 greenyellow = 173, 255, 47 honeydew = 240, 255, 240 hotpink = 255, 105, 180
    indianred = 205, 92, 92 indigo = 75, 0, 130 ivory = 255, 240, 240 khaki = 240, 230, 140 lavender = 230, 230, 250
    lavenderblush = 255, 240, 245 lawngreen = 124, 252, 0 lemonchiffon = 255, 250, 205 lightblue = 173, 216, 230 lightcoral = 240, 128, 128
    lightcyan = 224, 255, 255 lightgoldenrodyellow = 250, 250, 210 lightgreen = 144, 238, 144 lightgrey = 211, 211, 211 lightpink = 255, 182, 193
    lightsalmon = 255, 160, 122 lightseagreen = 32, 178, 170 lightskyblue = 135, 206, 250 lightslategray = 119, 136, 153 lightsteelblue = 176, 196, 222
    lightyellow = 255, 255, 224 lime = 0, 255, 0 limegreen = 50, 205, 50 linen = 250, 240, 230 magenta = 255, 0, 255
    maroon = 128, 0, 0 mediumaquamarine = 102, 205, 170 mediumblue = 0, 0, 205 mediumorchid = 186, 85, 211 mediumpurple = 147, 112, 219
    mediumseagreen = 60, 179, 113 mediumslateblue = 123, 104, 238 mediumspringgreen = 0, 250, 154 mediumturquoise = 72, 209, 204 mediumvioletred = 199, 21, 133
    midnightblue = 25, 25, 112 mintcream = 245, 255, 250 mistyrose = 255, 228, 225 moccasin = 255, 228, 181 navajowhite = 255, 222, 173
    navy = 0, 0, 128 oldlace = 253, 245, 230 olive = 128, 128, 0 olivedrab = 107, 142, 35 orange = 255, 165, 0
    orangered = 255, 69, 0 orchid = 218, 112, 214 palegoldenrod = 238, 232, 170 palegreen = 152, 251, 152 paleturquoise = 175, 238, 238
    palevioletred = 219, 112, 147 papayawhip = 255, 239, 213 peachpuff = 255, 239, 213 peru = 205, 133, 63 pink = 255, 192, 203
    plum = 221, 160, 221 powderblue = 176, 224, 230 purple = 128, 0, 128 red = 255, 0, 0 rosybrown = 188, 143, 143
    royalblue = 65, 105, 225 saddlebrown = 139, 69, 19 salmon = 250, 128, 114 sandybrown = 244, 164, 96 seagreen = 46, 139, 87
    seashell = 255, 245, 238 sienna = 160, 82, 45 silver = 192, 192, 192 skyblue = 135, 206, 235 slateblue = 106, 90, 205
    slategray = 112, 128, 144 snow = 255, 250, 250 springgreen = 0, 255, 127 steelblue = 70, 130, 180 tan = 210, 180, 140
    teal = 0, 128, 128 thistle = 216, 191, 216 tomato = 253, 99, 71 turquoise = 64, 224, 208 violet = 238, 130, 238
    wheat = 245, 222, 179 white = 255, 255, 255 whitesmoke = 245, 245, 245 yellow = 255, 255, 0 yellowgreen = 154, 205, 50 -
    - - diff --git a/doc/doc2/dump_molfile.html b/doc/doc2/dump_molfile.html deleted file mode 100644 index 07c3b9f881..0000000000 --- a/doc/doc2/dump_molfile.html +++ /dev/null @@ -1,138 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    dump molfile command -

    -

    Syntax: -

    -
    dump ID group-ID molfile N file format path 
-
    -
    • ID = user-assigned name for the dump - -
    • group-ID = ID of the group of atoms to be imaged - -
    • molfile = style of dump command (other styles atom or cfg or dcd or xtc or xyz or local or custom are discussed on the dump doc page) - -
    • N = dump every this many timesteps - -
    • file = name of file to write to - -
    • format = file format to be used - -
    • path = file path with plugins (optional) - - -
    -

    Examples: -

    -
    dump mf1 all molfile 10 melt1.xml hoomd
-dump mf2 all molfile 10 melt2-*.pdb pdb .
-dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile 
-
    -

    Description: -

    -

    Dump a snapshot of atom coordinates and selected additional quantities -to one or more files every N timesteps in one of several formats. -Only information for atoms in the specified group is dumped. This -specific dump style uses molfile plugins that are bundled with the -VMD molecular visualization and -analysis program. See Section tools of the -manual and the tools/lmp2vmd/README.txt file for more information -about support in VMD for reading and visualizing native LAMMPS dump -files. -

    -

    Unless the filename contains a * character, the output will be written -to one single file with the specified format. Otherwise there will be -one file per snapshot and the * will be replaced by the time step number -when the snapshot is written. -

    -

    IMPORTANT NOTE: Because periodic boundary conditions are enforced only -on timesteps when neighbor lists are rebuilt, the coordinates of an -atom written to a dump file may be slightly outside the simulation -box. -

    -

    The molfile plugin API has a few restrictions that have to be honored -by this dump style: the number of atoms must not change, the atoms -must be sorted, outside of the coordinates no change in atom properties -(like type, mass, charge) will be recorded. -

    -
    - -

    The format keyword determines what format is used to write out the -dump. For this to work, LAMMPS must be able to find and load a -compatible molfile plugin that supports this format. Settings made via -the dump_modify command can alter per atom properties -like element names. -

    -

    The path keyword determines which in directories. This is a "path" -like other search paths, i.e. it can contain multiple directories -separated by a colon (or semi-colon on windows). This keyword is -optional and default to ".", the current directory. -

    -

    The unwrap option of the dump_modify command allows -coordinates to be written "unwrapped" by the image flags for each atom. -Unwrapped means that if the atom has passed through a periodic boundary -one or more times, the value is printed for what the coordinate would be -if it had not been wrapped back into the periodic box. Note that these -coordinates may thus be far outside the box size stored with the -snapshot. -

    -
    - -

    Dumps are performed on timesteps that are a multiple of N (including -timestep 0) and on the last timestep of a minimization if the -minimization converges. Note that this means a dump will not be -performed on the initial timestep after the dump command is invoked, -if the current timestep is not a multiple of N. This behavior can be -changed via the dump_modify first command, which can -be useful if the dump command is invoked after a minimization ended on -an arbitrary timestep. N can be changed between runs by using the -dump_modify every command. The dump_modify -every command also allows a variable to be used to -determine the sequence of timesteps on which dump files are written. -

    -
    - -

    Restrictions: -

    -

    The molfile dump style is part of the USER-MOLFILE package. It is -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Molfile plugins provide a consistent programming interface to read and -write file formats commonly used in molecular simulations. The -USER-MOLFILE package only provides the interface code, not the plugins. -These can be obtained from a VMD installation which has to match the -platform that you are using to compile LAMMPS for. By adding plugins -to VMD, support for new file formats can be added to LAMMPS (or VMD -or other programs that use them) without having to recompile the -application itself. The plugins are installed in the directory: -/plugins//molfile -

    -

    NOTE: while the programming interface (API) to the plugins is backward -compatible, the binary interface (ABI) has been changing over time, so -it is necessary to compile this package with the plugin header files -from VMD that match the binary plugins. These header files in the -directory: /plugins/include For convenience, the package ships -with a set of header files that are compatible with VMD 1.9 and 1.9.1 -(June 2012) -

    -
    - -

    Related commands: -

    -

    dump, dump_modify, undump -

    -

    Default: -

    -

    The default path is ".". All other properties have to be specified. -

    - diff --git a/doc/doc2/echo.html b/doc/doc2/echo.html deleted file mode 100644 index 15ca28365e..0000000000 --- a/doc/doc2/echo.html +++ /dev/null @@ -1,43 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    echo command -

    -

    Syntax: -

    -
    echo style 
-
    -
    • style = none or screen or log or both -
    -

    Examples: -

    -
    echo both
-echo log 
-
    -

    Description: -

    -

    This command determines whether LAMMPS echoes each input script -command to the screen and/or log file as it is read and processed. If -an input script has errors, it can be useful to look at echoed output -to see the last command processed. -

    -

    The command-line switch -echo can be used -in place of this command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: -

    -
    echo log 
-
    - diff --git a/doc/doc2/fix.html b/doc/doc2/fix.html deleted file mode 100644 index 4658079d8e..0000000000 --- a/doc/doc2/fix.html +++ /dev/null @@ -1,280 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix command -

    -

    Syntax: -

    -
    fix ID group-ID style args 
-
    -
    • ID = user-assigned name for the fix -
    • group-ID = ID of the group of atoms to apply the fix to -
    • style = one of a long list of possible style names (see below) -
    • args = arguments used by a particular style -
    -

    Examples: -

    -
    fix 1 all nve
-fix 3 all nvt temp 300.0 300.0 0.01
-fix mine top setforce 0.0 NULL 0.0 
-
    -

    Description: -

    -

    Set a fix that will be applied to a group of atoms. In LAMMPS, a -"fix" is any operation that is applied to the system during -timestepping or minimization. Examples include updating of atom -positions and velocities due to time integration, controlling -temperature, applying constraint forces to atoms, enforcing boundary -conditions, computing diagnostics, etc. There are dozens of fixes -defined in LAMMPS and new ones can be added; see this -section for a discussion. -

    -

    Fixes perform their operations at different stages of the timestep. -If 2 or more fixes operate at the same stage of the timestep, they are -invoked in the order they were specified in the input script. -

    -

    The ID of a fix can only contain alphanumeric characters and -underscores. -

    -

    Fixes can be deleted with the unfix command. -

    -

    IMPORTANT NOTE: The unfix command is the only way to turn -off a fix; simply specifying a new fix with a similar style will not -turn off the first one. This is especially important to realize for -integration fixes. For example, using a fix nve -command for a second run after using a fix nvt command -for the first run, will not cancel out the NVT time integration -invoked by the "fix nvt" command. Thus two time integrators would be -in place! -

    -

    If you specify a new fix with the same ID and style as an existing -fix, the old fix is deleted and the new one is created (presumably -with new settings). This is the same as if an "unfix" command were -first performed on the old fix, except that the new fix is kept in the -same order relative to the existing fixes as the old one originally -was. Note that this operation also wipes out any additional changes -made to the old fix via the fix_modify command. -

    -

    The fix modify command allows settings for some -fixes to be reset. See the doc page for individual fixes for details. -

    -

    Some fixes store an internal "state" which is written to binary -restart files via the restart or -write_restart commands. This allows the fix to -continue on with its calculations in a restarted simulation. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file. See the doc pages -for individual fixes for info on which ones can be restarted. -

    -
    - -

    Some fixes calculate one of three styles of quantities: global, -per-atom, or local, which can be used by other commands or output as -described below. A global quantity is one or more system-wide values, -e.g. the energy of a wall interacting with particles. A per-atom -quantity is one or more values per atom, e.g. the displacement vector -for each atom since time 0. Per-atom values are set to 0.0 for atoms -not in the specified fix group. Local quantities are calculated by -each processor based on the atoms it owns, but there may be zero or -more per atoms. -

    -

    Note that a single fix may produces either global or per-atom or local -quantities (or none at all), but never more than one of these. -

    -

    Global, per-atom, and local quantities each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for each fix describes the style and kind of values it -produces, e.g. a per-atom vector. Some fixes produce more than one -kind of a single style, e.g. a global scalar and a global vector. -

    -

    When a fix quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID is the ID of the fix: -

    -
    - - -
    f_ID entire scalar, vector, or array
    f_ID[I] one element of vector, one column of array
    f_ID[I][J] one element of array -
    - -

    In other words, using one bracket reduces the dimension of the -quantity once (vector -> scalar, array -> vector). Using two brackets -reduces the dimension twice (array -> scalar). Thus a command that -uses scalar fix values as input can also process elements of a vector -or array. -

    -

    Note that commands and variables which use fix -quantities typically do not allow for all kinds, e.g. a command may -require a vector of values, not a scalar. This means there is no -ambiguity about referring to a fix quantity as f_ID even if it -produces, for example, both a scalar and vector. The doc pages for -various commands explain the details. -

    -
    - -

    In LAMMPS, the values generated by a fix can be used in several ways: -

    - -

    See this howto section for a summary of -various LAMMPS output options, many of which involve fixes. -

    -

    The results of fixes that calculate global quantities can be either -"intensive" or "extensive" values. Intensive means the value is -independent of the number of atoms in the simulation, -e.g. temperature. Extensive means the value scales with the number of -atoms in the simulation, e.g. total rotational kinetic energy. -Thermodynamic output will normalize extensive -values by the number of atoms in the system, depending on the -"thermo_modify norm" setting. It will not normalize intensive values. -If a fix value is accessed in another way, e.g. by a -variable, you may want to know whether it is an -intensive or extensive value. See the doc page for individual fixes -for further info. -

    -
    - -

    Each fix style has its own documentation page which describes its -arguments and what it does, as listed below. Here is an alphabetic -list of fix styles available in LAMMPS. They are also given in more -compact form in the Fix section of this -page. -

    -

    There are also additional fix styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the fix section -of this page. -

    -
    • adapt - change a simulation parameter over time -
    • addforce - add a force to each atom -
    • append/atoms - append atoms to a running simulation -
    • aveforce - add an averaged force to each atom -
    • ave/atom - compute per-atom time-averaged quantities -
    • ave/correlate - compute/output time correlations -
    • ave/histo - compute/output time-averaged histograms -
    • ave/spatial - compute/output time-averaged per-atom quantities by layer -
    • ave/time - compute/output global time-averaged quantities -
    • balance - perform dynamic load-balancing -
    • bond/break - break bonds on the fly -
    • bond/create - create bonds on the fly -
    • bond/swap - Monte Carlo bond swapping -
    • box/relax - relax box size during energy minimization -
    • deform - change the simulation box size/shape -
    • deposit - add new atoms above a surface -
    • drag - drag atoms towards a defined coordinate -
    • dt/reset - reset the timestep based on velocity, forces -
    • efield - impose electric field on system -
    • enforce2d - zero out z-dimension velocity and force -
    • evaporate - remove atoms from simulation periodically -
    • external - callback to an external driver program -
    • freeze - freeze atoms in a granular simulation -
    • gcmc - grand canonical insertions/deletions -
    • gld - generalized Langevin dynamics integrator -
    • gravity - add gravity to atoms in a granular simulation -
    • heat - add/subtract momentum-conserving heat -
    • indent - impose force due to an indenter -
    • langevin - Langevin temperature control -
    • lineforce - constrain atoms to move in a line -
    • momentum - zero the linear and/or angular momentum of a group of atoms -
    • move - move atoms in a prescribed fashion -
    • msst - multi-scale shock technique (MSST) integration -
    • neb - nudged elastic band (NEB) spring forces -
    • nph - constant NPH time integration via Nose/Hoover -
    • nphug - constant-stress Hugoniostat integration -
    • nph/asphere - NPH for aspherical particles -
    • nph/sphere - NPH for spherical particles -
    • npt - constant NPT time integration via Nose/Hoover -
    • npt/asphere - NPT for aspherical particles -
    • npt/sphere - NPT for spherical particles -
    • nve - constant NVE time integration -
    • nve/asphere - NVE for aspherical particles -
    • nve/asphere/noforce - NVE for aspherical particles without forces" -
    • nve/body - NVE for body particles -
    • nve/limit - NVE with limited step length -
    • nve/line - NVE for line segments -
    • nve/noforce - NVE without forces (v only) -
    • nve/sphere - NVE for spherical particles -
    • nve/tri - NVE for triangles -
    • nvt - constant NVT time integration via Nose/Hoover -
    • nvt/asphere - NVT for aspherical particles -
    • nvt/sllod - NVT for NEMD with SLLOD equations -
    • nvt/sphere - NVT for spherical particles -
    • orient/fcc - add grain boundary migration force -
    • planeforce - constrain atoms to move in a plane -
    • poems - constrain clusters of atoms to move as coupled rigid bodies -
    • pour - pour new atoms/molecules into a granular simulation domain -
    • press/berendsen - pressure control by Berendsen barostat -
    • print - print text and variables during a simulation -
    • property/atom - add customized per-atom values -
    • qeq/comb - charge equilibration for COMB potential qeq/dynamic - charge equilibration via dynamic method qeq/point - charge equilibration via point method qeq/shielded - charge equilibration via shielded method qeq/slater - charge equilibration via Slater method reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position of a group of atoms -
    • restrain - constrain a bond, angle, dihedral -
    • rigid - constrain one or more clusters of atoms to move as a rigid body with NVE integration -
    • rigid/nph - constrain one or more clusters of atoms to move as a rigid body with NPH integration -
    • rigid/npt - constrain one or more clusters of atoms to move as a rigid body with NPT integration -
    • rigid/nve - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration -
    • rigid/nvt - constrain one or more clusters of atoms to move as a rigid body with NVT integration -
    • rigid/small - constrain many small clusters of atoms to move as a rigid body with NVE integration -
    • setforce - set the force on each atom -
    • shake - SHAKE constraints on bonds and/or angles -
    • spring - apply harmonic spring force to group of atoms -
    • spring/rg - spring on radius of gyration of group of atoms -
    • spring/self - spring from each atom to its origin -
    • srd - stochastic rotation dynamics (SRD) -
    • store/force - store force on each atom -
    • store/state - store attributes for each atom -
    • temp/berendsen - temperature control by Berendsen thermostat -
    • temp/rescale - temperature control by velocity rescaling -
    • thermal/conductivity - Muller-Plathe kinetic energy exchange for thermal conductivity calculation -
    • tmd - guide a group of atoms to a new configuration -
    • ttm - two-temperature model for electronic/atomic coupling -
    • tune/kspace - auto-tune KSpace parameters -
    • vector - accumulate a global vector every N timesteps -
    • viscosity - Muller-Plathe momentum exchange for viscosity calculation -
    • viscous - viscous damping for granular simulations -
    • wall/colloid - Lennard-Jones wall interacting with finite-size particles -
    • wall/gran - frictional wall(s) for granular simulations -
    • wall/harmonic - harmonic spring wall -
    • wall/lj1043 - Lennard-Jones 10-4-3 wall -
    • wall/lj126 - Lennard-Jones 12-6 wall -
    • wall/lj93 - Lennard-Jones 9-3 wall -
    • wall/piston - moving reflective piston wall -
    • wall/reflect - reflecting wall(s) -
    • wall/region - use region surface as wall -
    • wall/srd - slip/no-slip wall for SRD particles -
    -

    Restrictions: -

    -

    Some fix styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info on packages. -The doc pages for individual fixes tell if it is part of a package. -

    -

    Related commands: -

    -

    unfix, fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_adapt.html b/doc/doc2/fix_adapt.html deleted file mode 100644 index 27e0e3322f..0000000000 --- a/doc/doc2/fix_adapt.html +++ /dev/null @@ -1,267 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix adapt command -

    -

    Syntax: -

    -
    fix ID group-ID adapt N attribute args ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • adapt = style name of this fix command - -
    • N = adapt simulation settings every this many timesteps - -
    • one or more attribute/arg pairs may be appended - -
    • attribute = pair or kspace or atom - -
        pair args = pstyle pparam I J v_name
-    pstyle = pair style name, e.g. lj/cut
-    pparam = parameter to adapt over time
-    I,J = type pair(s) to set parameter for
-    v_name = variable with name that calculates value of pparam
-  kspace arg = v_name
-    v_name = variable with name that calculates scale factor on K-space terms
-  atom args = aparam v_name
-    aparam = parameter to adapt over time
-    v_name = variable with name that calculates value of aparam 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = scale or reset - -
        scale value = no or yes
-    no = the variable value is the new setting
-    yes = the variable value multiplies the original setting
-  reset value = no or yes
-    no = values will remain altered at the end of a run
-    yes = reset altered values to their original values at the end of a run 
-
      - -
    -

    Examples: -

    -
    fix 1 all adapt 1 pair soft a 1 1 v_prefactor
-fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
-fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
-fix 1 all adapt 10 atom diameter v_size 
-
    -

    Description: -

    -

    Change or adapt one or more specific simulation attributes or settings -over time as a simulation runs. Pair potential and K-space and atom -attributes which can be varied by this fix are discussed below. Many -other fixes can also be used to time-vary simulation parameters, -e.g. the "fix deform" command will change the simulation box -size/shape and the "fix move" command will change atom positions and -velocities in a prescribed manner. Also note that many commands allow -variables as arguments for specific parameters, if described in that -manner on their doc pages. An equal-style variable can calculate a -time-dependent quantity, so this is another way to vary a simulation -parameter over time. -

    -

    If N is specified as 0, the specified attributes are only changed -once, before the simulation begins. This is all that is needed if the -associated variables are not time-dependent. If N > 0, then changes -are made every N steps during the simulation, presumably with a -variable that is time-dependent. -

    -

    Depending on the value of the reset keyword, attributes changed by -this fix will or will not be reset back to their original values at -the end of a simulation. Even if reset is specified as yes, a -restart file written during a simulation will contain the modified -settings. -

    -

    If the scale keyword is set to no, then the value the parameter is -set to will be whatever the variable generates. If the scale -keyword is set to yes, then the value of the altered parameter will -be the initial value of that parameter multiplied by whatever the -variable generates. I.e. the variable is now a "scale factor" applied -in (presumably) a time-varying fashion to the parameter. -

    -

    Note that whether scale is no or yes, internally, the parameters -themselves are actually altered by this fix. Make sure you use the -reset yes option if you want the parameters to be restored to their -initial values after the run. -

    -
    - -

    The pair keyword enables various parameters of potentials defined by -the pair_style command to be changed, if the pair -style supports it. Note that the pair_style and -pair_coeff commands must be used in the usual manner -to specify these parameters initially; the fix adapt command simply -overrides the parameters. -

    -

    The pstyle argument is the name of the pair style. If pair_style -hybrid or hybrid/overlay is used, pstyle should be -a sub-style name. If there are multiple sub-styles using the same -pair style, then pstyle should be specified as "style:N" where N is -which instance of the pair style you wish to adapt, e.g. the first, -second, etc. For example, pstyle could be specified as "soft" or -"lubricate" or "lj/cut:1" or "lj/cut:2". The pparam argument is the -name of the parameter to change. This is the current list of pair -styles and parameters that can be varied by this fix. See the doc -pages for individual pair styles and their energy formulas for the -meaning of these parameters: -

    -
    - - - - - - - - - - -
    born a,b,c type pairs
    buck a,c type pairs
    coul/cut scale type pairs
    coul/debye scale type pairs
    coul/long scale type pairs
    lj/cut epsilon,sigma type pairs
    lj/expand epsilon,sigma,delta type pairs
    lubricate mu global
    gauss a type pairs
    morse d0,r0,alpha type pairs
    soft a type pairs -
    - -

    IMPORTANT NOTE: It is easy to add new potentials and their parameters -to this list. All it typically takes is adding an extract() method to -the pair_*.cpp file associated with the potential. -

    -

    Some parameters are global settings for the pair style, e.g. the -viscosity setting "mu" for pair_style lubricate. -Other parameters apply to atom type pairs within the pair style, -e.g. the prefactor "a" for pair_style soft. -

    -

    Note that for many of the potentials, the parameter that can be varied -is effectively a prefactor on the entire energy expression for the -potential, e.g. the lj/cut epsilon. The parameters listed as "scale" -are exactly that, since the energy expression for the -coul/cut potential (for example) has no labeled -prefactor in its formula. To apply an effective prefactor to some -potentials, multiple parameters need to be altered. For example, the -Buckingham potential needs both the A and C terms -altered together. To scale the Buckingham potential, you should thus -list the pair style twice, once for A and once for C. -

    -

    If a type pair parameter is specified, the I and J settings should -be specified to indicate which type pairs to apply it to. If a global -parameter is specified, the I and J settings still need to be -specified, but are ignored. -

    -

    Similar to the pair_coeff command, I and J can be -specified in one of two ways. Explicit numeric values can be used for -each, as in the 1st example above. I <= J is required. LAMMPS sets -the coefficients for the symmetric J,I interaction to the same values. -

    -

    A wild-card asterisk can be used in place of or in conjunction with -the I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. -

    -

    IMPROTANT NOTE: If pair_style hybrid or -hybrid/overlay is being used, then the pstyle will -be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the pair_coeff -command) for that sub-style. -

    -

    The v_name argument for keyword pair is the name of an -equal-style variable which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. Equal-style -variables can specify formulas with various mathematical functions, -and include thermo_style command keywords for the -simulation box parameters and timestep and elapsed time. Thus it is -easy to specify parameters that change as a function of time or span -consecutive runs in a continuous fashion. For the latter, see the -start and stop keywords of the run command and the -elaplong keyword of thermo_style custom for -details. -

    -

    For example, these commands would change the prefactor coefficient of -the pair_style soft potential from 10.0 to 30.0 in a -linear fashion over the course of a simulation: -

    -
    variable prefactor equal ramp(10,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor 
-
    -
    - -

    The kspace keyword used the specified variable as a scale factor on -the energy, forces, virial calculated by whatever K-Space solver is -defined by the kspace_style command. If the -variable has a value of 1.0, then the solver is unaltered. -

    -

    The kspace keyword works this way whether the scale keyword -is set to no or yes. -

    -
    - -

    The atom keyword enables various atom properties to be changed. The -aparam argument is the name of the parameter to change. This is the -current list of atom parameters that can be varied by this fix: -

    -
    • charge = charge on particle -
    • diameter = diameter of particle -
    -

    The v_name argument of the atom keyword is the name of an -equal-style variable which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. See the -discussion above describing the formulas associated with equal-style -variables. The new value is assigned to the corresponding attribute -for all atoms in the fix group. -

    -

    IMPORTANT NOTE: The atom keyword works this way whether the scale -keyword is set to no or yes. I.e. the use of scale yes is not yet -supported by the atom keyword. -

    -

    If the atom parameter is diameter and per-atom density and per-atom -mass are defined for particles (e.g. atom_style -granular), then the mass of each particle is also -changed when the diameter changes (density is assumed to stay -constant). -

    -

    For example, these commands would shrink the diameter of all granular -particles in the "center" group from 1.0 to 0.1 in a linear fashion -over the course of a 1000-step simulation: -

    -
    variable size equal ramp(1.0,0.1)
-fix 1 center adapt 10 atom diameter v_size 
-
    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    For rRESPA time integration, this fix changes -parameters on the outermost rRESPA level. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute ti -

    -

    Default: -

    -

    The option defaults are scale = no, reset = no. -

    - diff --git a/doc/doc2/fix_adapt_fep.html b/doc/doc2/fix_adapt_fep.html deleted file mode 100644 index a1e3009c1d..0000000000 --- a/doc/doc2/fix_adapt_fep.html +++ /dev/null @@ -1,275 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix adapt/fep command -

    -

    Syntax: -

    -
    fix ID group-ID adapt/fep N attribute args ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • adapt/fep = style name of this fix command - -
    • N = adapt simulation settings every this many timesteps - -
    • one or more attribute/arg pairs may be appended - -
    • attribute = pair or kspace or atom - -
        pair args = pstyle pparam I J v_name
-    pstyle = pair style name, e.g. lj/cut
-    pparam = parameter to adapt over time
-    I,J = type pair(s) to set parameter for
-    v_name = variable with name that calculates value of pparam
-  kspace arg = v_name
-    v_name = variable with name that calculates scale factor on K-space terms
-  atom args = aparam v_name
-    aparam = parameter to adapt over time
-    I = type(s) to set parameter for
-    v_name = variable with name that calculates value of aparam 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = scale or reset or after - -
        scale value = no or yes
-    no = the variable value is the new setting
-    yes = the variable value multiplies the original setting
-  reset value = no or yes
-    no = values will remain altered at the end of a run
-    yes = reset altered values to their original values at the end
-    of a run
-  after value = no or yes
-    no = parameters are adapted at timestep N
-    yes = parameters are adapted one timestep after N 
-
      - -
    -

    Examples: -

    -
    fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
-fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
-fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
-fix 1 all adapt/fep 10 atom diameter 1 v_size 
-
    -

    Description: -

    -

    Change or adapt one or more specific simulation attributes or settings -over time as a simulation runs. -

    -

    This is an enhanced version of the fix_adapt command -with two differences, -

    -
    • It is possible to modify the charges of chosen atom types only, -instead of scaling all the charges in the system. - -
    • There is a new option after for better compatibility with "fix -ave/time". -
    -

    This version is suited for free energy calculations using -compute_ti or compute_fep. -

    -

    If N is specified as 0, the specified attributes are only changed -once, before the simulation begins. This is all that is needed if the -associated variables are not time-dependent. If N > 0, then changes -are made every N steps during the simulation, presumably with a -variable that is time-dependent. -

    -

    Depending on the value of the reset keyword, attributes changed by -this fix will or will not be reset back to their original values at -the end of a simulation. Even if reset is specified as yes, a -restart file written during a simulation will contain the modified -settings. -

    -

    If the scale keyword is set to no, then the value the parameter is -set to will be whatever the variable generates. If the scale -keyword is set to yes, then the value of the altered parameter will -be the initial value of that parameter multiplied by whatever the -variable generates. I.e. the variable is now a "scale factor" applied -in (presumably) a time-varying fashion to the parameter. Internally, -the parameters themselves are actually altered; make sure you use the -reset yes option if you want the parameters to be restored to their -initial values after the run. -

    -

    If the after keyword is set to yes, then the parameters are -changed one timestep after the multiple of N. In this manner, if a fix -such as "fix ave/time" is used to calculate averages at every N -timesteps, all the contributions to the average will be obtained with -the same values of the parameters. -

    -
    - -

    The pair keyword enables various parameters of potentials defined by -the pair_style command to be changed, if the pair -style supports it. Note that the pair_style and -pair_coeff commands must be used in the usual manner -to specify these parameters initially; the fix adapt command simply -overrides the parameters. -

    -

    The pstyle argument is the name of the pair style. If pair_style -hybrid or hybrid/overlay is used, pstyle should be -a sub-style name. For example, pstyle could be specified as "soft" -or "lubricate". The pparam argument is the name of the parameter to -change. This is the current list of pair styles and parameters that -can be varied by this fix. See the doc pages for individual pair -styles and their energy formulas for the meaning of these parameters: -

    -
    - - - - - - - - - -
    born a,b,c type pairs
    buck a,c type pairs
    coul/cut scale type pairs
    coul/debye scale type pairs
    coul/long scale type pairs
    lj/cut epsilon,sigma type pairs
    lj/expand epsilon,sigma,delta type pairs
    lubricate mu global
    gauss a type pairs
    soft a type pairs -
    - -

    IMPORTANT NOTE: It is easy to add new potentials and their parameters -to this list. All it typically takes is adding an extract() method to -the pair_*.cpp file associated with the potential. -

    -

    Some parameters are global settings for the pair style, e.g. the -viscosity setting "mu" for pair_style lubricate. -Other parameters apply to atom type pairs within the pair style, -e.g. the prefactor "a" for pair_style soft. -

    -

    Note that for many of the potentials, the parameter that can be varied -is effectively a prefactor on the entire energy expression for the -potential, e.g. the lj/cut epsilon. The parameters listed as "scale" -are exactly that, since the energy expression for the -coul/cut potential (for example) has no labeled -prefactor in its formula. To apply an effective prefactor to some -potentials, multiple parameters need to be altered. For example, the -Buckingham potential needs both the A and C terms -altered together. To scale the Buckingham potential, you should thus -list the pair style twice, once for A and once for C. -

    -

    If a type pair parameter is specified, the I and J settings should -be specified to indicate which type pairs to apply it to. If a global -parameter is specified, the I and J settings still need to be -specified, but are ignored. -

    -

    Similar to the pair_coeff command, I and J can be -specified in one of two ways. Explicit numeric values can be used for -each, as in the 1st example above. I <= J is required. LAMMPS sets -the coefficients for the symmetric J,I interaction to the same values. -

    -

    A wild-card asterisk can be used in place of or in conjunction with -the I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. -

    -

    IMPROTANT NOTE: If pair_style hybrid or -hybrid/overlay is being used, then the pstyle will -be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the pair_coeff -command) for that sub-style. -

    -

    The v_name argument for keyword pair is the name of an -equal-style variable which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. Equal-style -variables can specify formulas with various mathematical functions, -and include thermo_style command keywords for the -simulation box parameters and timestep and elapsed time. Thus it is -easy to specify parameters that change as a function of time or span -consecutive runs in a continuous fashion. For the latter, see the -start and stop keywords of the run command and the -elaplong keyword of thermo_style custom for -details. -

    -

    For example, these commands would change the prefactor coefficient of -the pair_style soft potential from 10.0 to 30.0 in a -linear fashion over the course of a simulation: -

    -
    variable prefactor equal ramp(10,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor 
-
    -
    - -

    The kspace keyword used the specified variable as a scale factor on -the energy, forces, virial calculated by whatever K-Space solver is -defined by the kspace_style command. If the -variable has a value of 1.0, then the solver is unaltered. -

    -

    The kspace keyword works this way whether the scale keyword -is set to no or yes. -

    -
    - -

    The atom keyword enables various atom properties to be changed. The -aparam argument is the name of the parameter to change. This is the -current list of atom parameters that can be varied by this fix: -

    -
    • charge = charge on particle -
    • diameter = diameter of particle -
    -

    The I argument indicates which atom types are affected. A wild-card -asterisk can be used in place of or in conjunction with the I argument -to set the coefficients for multiple atom types. -

    -

    The v_name argument of the atom keyword is the name of an -equal-style variable which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. See the -discussion above describing the formulas associated with equal-style -variables. The new value is assigned to the corresponding attribute -for all atoms in the fix group. -

    -

    If the atom parameter is diameter and per-atom density and per-atom -mass are defined for particles (e.g. atom_style -granular), then the mass of each particle is also -changed when the diameter changes (density is assumed to stay -constant). -

    -

    For example, these commands would shrink the diameter of all granular -particles in the "center" group from 1.0 to 0.1 in a linear fashion -over the course of a 1000-step simulation: -

    -
    variable size equal ramp(1.0,0.1)
-fix 1 center adapt 10 atom diameter * v_size 
-
    -

    For rRESPA time integration, this fix changes -parameters on the outermost rRESPA level. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute fep, fix_adapt, compute -ti -

    -

    Default: -

    -

    The option defaults are scale = no, reset = no, after = no. -

    - diff --git a/doc/doc2/fix_addforce.html b/doc/doc2/fix_addforce.html deleted file mode 100644 index e6ba94273f..0000000000 --- a/doc/doc2/fix_addforce.html +++ /dev/null @@ -1,184 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix addforce command -

    -

    fix addforce/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID addforce fx fy fz keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • addforce = style name of this fix command - -
    • fx,fy,fz = force component values (force units) - -
        any of fx,fy,fz can be a variable (see below) 
-
      -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = every or region or energy - -
        every value = Nevery
-    Nevery = add force every this many timesteps
-  region value = region-ID
-    region-ID = ID of region atoms must be in to have added force
-  energy value = v_name
-    v_name = variable with name that calculates the potential energy of each atom in the added force field 
-
      - -
    -

    Examples: -

    -
    fix kick flow addforce 1.0 0.0 0.0
-fix kick flow addforce 1.0 0.0 v_oscillate
-fix ff boundary addforce 0.0 0.0 v_push energy v_espace 
-
    -

    Description: -

    -

    Add fx,fy,fz to the corresponding component of force for each atom in -the group. This command can be used to give an additional push to -atoms in a simulation, such as for a simulation of Poiseuille flow in -a channel. -

    -

    Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style variable, namely fx, -fy, fz. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value(s) used to determine -the force component. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent force field. -

    -

    Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent force -field with optional time-dependence as well. -

    -

    If the every keyword is used, the Nevery setting determines how -often the forces are applied. The default value is 1, for every -timestep. -

    -

    If the region keyword is used, the atom must also be in the -specified geometric region in order to have force added -to it. -

    -
    - -

    Adding a force to atoms implies a change in their potential energy as -they move due to the applied force field. For dynamics via the "run" -command, this energy can be optionally added to the system's potential -energy for thermodynamic output (see below). For energy minimization -via the "minimize" command, this energy must be added to the system's -potential energy to formulate a self-consistent minimization problem -(see below). -

    -

    The energy keyword is not allowed if the added force is a constant -vector F = (fx,fy,fz), with all components defined as numeric -constants and not as variables. This is because LAMMPS can compute -the energy for each atom directly as E = -x dot F = -(x*fx + y*fy + -z*fz), so that -Grad(E) = F. -

    -

    The energy keyword is optional if the added force is defined with -one or more variables, and if you are performing dynamics via the -run command. If the keyword is not used, LAMMPS will set -the energy to 0.0, which is typically fine for dynamics. -

    -

    The energy keyword is required if the added force is defined with -one or more variables, and you are performing energy minimization via -the "minimize" command. The keyword specifies the name of an -atom-style variable which is used to compute the -energy of each atom as function of its position. Like variables used -for fx, fy, fz, the energy variable is specified as v_name, -where name is the variable name. -

    -

    Note that when the energy keyword is used during an energy -minimization, you must insure that the formula defined for the -atom-style variable is consistent with the force -variable formulas, i.e. that -Grad(E) = F. For example, if the force -were a spring-like F = kx, then the energy formula should be E = --0.5kx^2. If you don't do this correctly, the minimization will not -converge properly. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the potential "energy" inferred by the added force to the -system's potential energy as part of thermodynamic -output. This is a fictitious quantity but is -needed so that the minimize command can include the -forces added by this fix in a consistent manner. I.e. there is a -decrease in potential energy when atoms move in the direction of the -added force. -

    -

    This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various output -commands. The scalar is the potential -energy discussed above. The vector is the total force on the group of -atoms before the forces on individual atoms are changed by the fix. -The scalar and vector values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. -

    -

    IMPORTANT NOTE: If you want the fictitious potential energy associated -with the added forces to be included in the total potential energy of -the system (the quantity being minimized), you MUST enable the -fix_modify energy option for this fix. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix setforce, fix aveforce -

    -

    Default: -

    -

    The option default for the every keyword is every = 1. -

    - diff --git a/doc/doc2/fix_addtorque.html b/doc/doc2/fix_addtorque.html deleted file mode 100644 index a9a521e3b7..0000000000 --- a/doc/doc2/fix_addtorque.html +++ /dev/null @@ -1,102 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix addtorque command -

    -

    Syntax: -

    -
    fix ID group-ID addtorque Tx Ty Tz 
-
    -
    • ID, group-ID are documented in fix command - -
    • addtorque = style name of this fix command - -
    • Tx,Ty,Tz = torque component values (torque units) - -
    • any of Tx,Ty,Tz can be a variable (see below) - - -
    -

    Examples: -

    -
    fix kick bead addtorque 2.0 3.0 5.0
-fix kick bead addtorque 0.0 0.0 v_oscillate 
-
    -

    Description: -

    -

    Add a set of forces to each atom in -the group such that: -

    -
    • the components of the total torque applied on the group (around its -center of mass) are Tx,Ty,Tz - -
    • the group would move as a rigid body in the absence of other -forces. -
    -

    This command can be used to drive a group of atoms into rotation. -

    -

    Any of the 3 quantities defining the torque components can be specified -as an equal-style variable, namely Tx, -Ty, Tz. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -torque component. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent torque. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the potential "energy" inferred by the added forces to the -system's potential energy as part of thermodynamic -output. This is a fictitious quantity but is -needed so that the minimize command can include the -forces added by this fix in a consistent manner. I.e. there is a -decrease in potential energy when atoms move in the direction of the -added forces. -

    -

    This fix computes a global scalar and a global 3-vector, which can be -accessed by various output commands. -The scalar is the potential energy discussed above. The vector is the -total torque on the group of atoms before the forces on individual -atoms are changed by the fix. The scalar and vector values calculated -by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix addforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_append_atoms.html b/doc/doc2/fix_append_atoms.html deleted file mode 100644 index f2df056748..0000000000 --- a/doc/doc2/fix_append_atoms.html +++ /dev/null @@ -1,123 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix append/atoms command -

    -

    Syntax: -

    -
    fix ID group-ID append/atoms face ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • append/atoms = style name of this fix command - -
    • face = zhi - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = basis or size or freq or temp or random or units - -
        basis values = M itype
-    M = which basis atom
-    itype = atom type (1-N) to assign to this basis atom
-  size args = Lz
-    Lz = z size of lattice region appended in a single event(distance units)
-  freq args = freq
-    freq = the number of timesteps between append events
-  temp args = target damp seed extent
-    target = target temperature for the region between zhi-extent and zhi (temperature units)
-    damp = damping parameter (time units)
-    seed = random number seed for langevin kicks
-    extent = extent of thermostated region (distance units)
-  random args = xmax ymax zmax seed
-    xmax, ymax, zmax = maximum displacement in particular direction (distance units)
-    seed = random number seed for random displacement
-  units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    fix 1 all append/atoms zhi size 5.0 freq 295 units lattice
-fix 4 all append/atoms zhi size 15.0 freq 5 units box
-fix A all append/atoms zhi size 1.0 freq 1000 units lattice 
-
    -

    Description: -

    -

    This fix creates atoms on a lattice, appended on the zhi edge of the -system box. This can be useful when a shock or wave is propagating -from zlo. This allows the system to grow with time to accommodate an -expanding wave. A simulation box must already exist, which is -typically created via the create_box command. -Before using this command, a lattice must also be defined using the -lattice command. -

    -

    This fix will automatically freeze atoms on the zhi edge of the -system, so that overlaps are avoided when new atoms are appended. -

    -

    The basis keyword specifies an atom type that will be assigned to -specific basis atoms as they are created. See the -lattice command for specifics on how basis atoms are -defined for the unit cell of the lattice. By default, all created -atoms are assigned type = 1 unless this keyword specifies differently. -

    -

    The size keyword defines the size in z of the chunk of material to -be added. -

    -

    The random keyword will give the atoms random displacements around -their lattice points to simulate some initial temperature. -

    -

    The temp keyword will cause a region to be thermostated with a -Langevin thermostat on the zhi boundary. The size of the region is -measured from zhi and is set with the extent argument. -

    -

    The units keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant is used. -A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacings. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    The boundary on which atoms are added with append/atoms must be -shrink/minimum. The opposite boundary may be any boundary type other -than periodic. -

    -

    Related commands: -

    -

    fix wall/piston command -

    -

    Default: -

    -

    The keyword defaults are size = 0.0, freq = 0, units = lattice. All -added atoms are of type 1 unless the basis keyword is used. -

    - diff --git a/doc/doc2/fix_atc.html b/doc/doc2/fix_atc.html deleted file mode 100644 index 86db400873..0000000000 --- a/doc/doc2/fix_atc.html +++ /dev/null @@ -1,258 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix atc command -

    -

    Syntax: -

    -
    fix   atc   
-
    -
  • fixID = name of fix - -
  • group = name of group fix is to be applied - -
  • type = thermal or two_temperature or hardy or field - -
     thermal = thermal coupling with fields: temperature
- two_temperature = electron-phonon coupling with field: temperature and electron_temperature
- hardy = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) 
- field = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) 
-
    -
  • parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file - -

    Examples: -

    -
    fix AtC internal atc thermal Ar_thermal.dat 
-fix AtC internal atc two_temperature Ar_ttm.mat
-fix AtC internal atc hardy
-fix AtC internal atc field 
-
    -

    Description: -

    -

    This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. -

    -
    -
    -
    The following coupling example is typical, but non-exhaustive:
- # ... commands to create and initialize the MD system 
-
    -
     # initial fix to designate coupling type and group to apply it to 
- # tag group physics material_file 
- fix AtC internal atc thermal Ar_thermal.mat 
-
    -
     # create a uniform 12 x 2 x 2 mesh that covers region contain the group 
- # nx ny nz region periodicity 
- fix_modify AtC mesh create 12 2 2 mdRegion f p p 
-
    -
     # specify the control method for the type of coupling 
- # physics control_type 
- fix_modify AtC thermal control flux 
-
    -
     # specify the initial values for the empirical field "temperature" 
- # field node_group value 
- fix_modify AtC initial temperature all 30 
-
    -
     # create an output stream for nodal fields 
- # filename output_frequency 
- fix_modify AtC output atc_fe_output 100 
-
    -
     run 1000 
-
    -

    likewise for this post-processing example: -

    -
     # ... commands to create and initialize the MD system 
-
    -
     # initial fix to designate post-processing and the group to apply it to 
- # no material file is allowed nor required 
- fix AtC internal atc hardy 
-
    -
     # for hardy fix, specific kernel function (function type and range) to # be used as a localization function 
- fix AtC kernel quartic_sphere 10.0 
-
    -
     # create a uniform 1 x 1 x 1 mesh that covers region contain the group 
- # with periodicity this effectively creats a system average 
- fix_modify AtC mesh create 1 1 1 box p p p 
-
    -
     # change from default lagrangian map to eulerian 
- # refreshed every 100 steps 
- fix_modify AtC atom_element_map eulerian 100 
-
    -
     # start with no field defined 
- # add mass density, potential energy density, stress and temperature 
- fix_modify AtC fields add density energy stress temperature 
-
    -
     # create an output stream for nodal fields 
- # filename output_frequency 
- fix_modify AtC output nvtFE 100 text 
-
    -
     run 1000 
-
    -

    the mesh's linear interpolation functions can be used as the localization function - by using the field option: -

    -

    fix AtC internal atc field -

    -

    fix_modify AtC mesh create 1 1 1 box p p p -

    -

    ... -

    -

    Note coupling and post-processing can be combined in the same simulations using separate fixes. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart files. The fix_modify options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. -

    -
    • Currently, -
    • - the coupling is restricted to thermal physics -
    • - the FE computations are done in serial on each processor. -
    -

    Related commands: -

    -

    After specifying this fix in your input script, several other fix_modify commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. -

    -

    fix_modify commands for setup: -

    - -

    fix_modify commands for boundary and initial conditions: -

    - -

    fix_modify commands for control and filtering: -

    - -

    fix_modify commands for output: -

    - -

    fix_modify commands for post-processing: -

    - -

    miscellaneous fix_modify commands: -

    - -

    Note: a set of example input files with the attendant material files are included with this package -

    -

    Default: -None -

    -
    - -

    For detailed exposition of the theory and algorithms please see: -

    - - -

    (Wagner) Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. -

    - - -

    (Zimmerman2004) Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. -

    - - -

    (Zimmerman2010) Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364. -

    - - -

    (Templeton2010) Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. -

    - - -

    (Jones) Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940. -

    - - -

    (Templeton2011) Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736. -

    - - -

    (Mandadapu) Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. -

    -

    Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation. -

    - diff --git a/doc/doc2/fix_atom_swap.html b/doc/doc2/fix_atom_swap.html deleted file mode 100644 index 1d01b66043..0000000000 --- a/doc/doc2/fix_atom_swap.html +++ /dev/null @@ -1,201 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix atom/swap command -

    -

    Syntax: -

    -
    fix ID group-ID atom/swap N X seed T keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • atom/swap = style name of this fix command - -
    • N = invoke this fix every N steps - -
    • X = number of swaps to attempt every N steps - -
    • seed = random # seed (positive integer) - -
    • T = scaling temperature of the MC swaps (temperature units) - -
    • one or more keyword/value pairs may be appended to args - -
    • keyword = types or mu or ke or semi-grand or region - -
        types values = two or more atom types
-  mu values = chemical potential of swap types (energy units)
-  ke value = no or yes
-    no = no conservation of kinetic energy after atom swaps
-    yes = kinetic energy is conserved after atom swaps
-  semi-grand value = no or yes
-    no = particle type counts and fractions conserved
-    yes = semi-grand canonical ensemble, particle fractions not conserved
-  region value = region-ID
-    region-ID = ID of region to use as an exchange/move volume 
-
      - -
    -

    Examples: -

    -
    fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
-fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6 
-fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0 
-
    -

    Description: -

    -

    This fix performs Monte Carlo swaps of atoms of one given atom type -with atoms of the other given atom types. The specified T is used in -the Metropolis criterion dictating swap probabilities. -

    -

    Perform X swaps of atoms of one type with atoms of another type -according to a Monte Carlo probability. Swap candidates must be in the -fix group, must be in the region (if specified), and must be of one of -the listed types. Swaps are attempted between candidates that are -chosen randomly with equal probability among the candidate -atoms. Swaps are not attempted between atoms of the same type since -nothing would happen. -

    -

    All atoms in the simulation domain can be moved using regular time -integration displacements, e.g. via fix_nvt, resulting -in a hybrid MC+MD simulation. A smaller-than-usual timestep size may -be needed when running such a hybrid simulation, especially if the -swapped atoms are not well equilibrated. -

    -

    The types keyword is required. At least two atom types must be -specified. -

    -

    The ke keyword can be set to no to turn off kinetic energy -conservation for swaps. The default is yes, which means that swapped -atoms have their velocities scaled by the ratio of the masses of the -swapped atom types. This ensures that the kinetic energy of each atom -is the same after the swap as it was before the swap, even though the -atom masses have changed. -

    -

    The semi-grand keyword can be set to yes to switch to the -semi-grand canonical ensemble as discussed in (Sadigh). This -means that the total number of each particle type does not need to be -conserved. The default is no, which means that the only kind of swap -allowed exchanges an atom of one type with an atom of a different -given type. In other words, the relative mole fractions of the swapped -atoms remains constant. Whereas in the semi-grand canonical ensemble, -the composition of the system can change. Note that when using -semi-grand, atoms in the fix group whose type is not listed -in the types keyword are ineligible for attempted -conversion. An attempt is made to switch -the selected atom (if eligible) to one of the other listed types -with equal probability. Acceptance of each attempt depends upon the Metropolis criterion. -

    -

    The mu keyword allows users to specify chemical -potentials. This is required and allowed only when using semi-grand. -All chemical potentials are absolute, so there is one for -each swap type listed following the types keyword. -In semi-grand canonical ensemble simulations the chemical composition -of the system is controlled by the difference in these values. So -shifting all values by a constant amount will have no effect -on the simulation. -

    -

    This command may optionally use the region keyword to define swap -volume. The specified region must have been previously defined with a -region command. It must be defined with side = in. -Swap attempts occur only between atoms that are both within the -specified region. Swaps are not otherwise attempted. -

    -

    You should ensure you do not swap atoms belonging to a molecule, or -LAMMPS will soon generate an error when it tries to find those atoms. -LAMMPS will warn you if any of the atoms eligible for swapping have a -non-zero molecule ID, but does not check for this at the time of -swapping. -

    -

    If not using semi-grand this fix checks to ensure all atoms of the -given types have the same atomic charge. LAMMPS doesn't enforce this -in general, but it is needed for this fix to simplify the -swapping procedure. Successful swaps will swap the atom type and charge -of the swapped atoms. Conversely, when using semi-grand, it is assumed that all the atom -types involved in switches have the same charge. Otherwise, charge -would not be conserved. As a consequence, no checks on atomic charges are -performed, and successful switches update the atom type but not the -atom charge. While it is possible to use semi-grand with groups of -atoms that have different charges, these charges will not be changed when the -atom types change. -

    -

    Since this fix computes total potential energies before and after -proposed swaps, so even complicated potential energy calculations are -OK, including the following: -

    -
    • long-range electrostatics (kspace) -
    • many body pair styles -
    • hybrid pair styles -
    • eam pair styles -
    • triclinic systems -
    • need to include potential energy contributions from other fixes -
    -

    Some fixes have an associated potential energy. Examples of such fixes -include: efield, gravity, -addforce, langevin, -restrain, temp/berendsen, -temp/rescale, and wall fixes. -For that energy to be included in the total potential energy of the -system (the quantity used when performing GCMC moves), -you MUST enable the fix_modify energy option for -that fix. The doc pages for individual fix commands -specify if this should be done. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the fix to binary restart -files. This includes information about the random -number generator seed, the next timestep for MC exchanges, etc. See -the read_restart command for info on how to -re-specify a fix in an input script that reads a restart file, so that -the operation of the fix continues in an uninterrupted fashion. -

    -

    None of the fix_modify options are relevant to this -fix. -

    -

    This fix computes a global vector of length 2, which can be accessed -by various output commands. The vector -values are the following global cumulative quantities: -

    -
    • 1 = swap attempts -
    • 2 = swap successes -
    -

    The vector values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix_nvt, neighbor, -fix_deposit, fix_evaporate, -delete_atoms, fix_gcmc -

    -

    Default: -

    -

    The option defaults are ke = yes, semi-grand = no, mu = 0.0 for -all atom types. -

    -
    - - - -

    (Sadigh) B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and -L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012). -

    - diff --git a/doc/doc2/fix_ave_atom.html b/doc/doc2/fix_ave_atom.html deleted file mode 100644 index 88a6b22cfe..0000000000 --- a/doc/doc2/fix_ave_atom.html +++ /dev/null @@ -1,165 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/atom command -

    -

    Syntax: -

    -
    fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ave/atom = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of times to use input values for calculating averages - -
    • Nfreq = calculate averages every this many timesteps -one or more input values can be listed - -
    • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name - -
        x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/atom 1 100 100 vx vy vz
-fix 1 all ave/atom 10 20 1000 c_my_stress[1] 
-
    -

    Description: -

    -

    Use one or more per-atom vectors as inputs every few timesteps, and -average them atom by atom over longer timescales. The resulting -per-atom averages can be used by other output -commands such as the fix -ave/spatial or dump custom commands. -

    -

    The group specified with the command means only atoms within the group -have their averages computed. Results are set to 0.0 for atoms not in -the group. -

    -

    Each input value can be an atom attribute (position, velocity, force -component) or can be the result of a compute or -fix or the evaluation of an atom-style -variable. In the latter cases, the compute, fix, or -variable must produce a per-atom vector, not a global quantity or -local quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the fix -ave/time command. -

    -

    Computes that produce per-atom vectors or arrays are -those which have the word atom in their style name. See the doc -pages for individual fixes to determine which ones produce -per-atom vectors or arrays. Variables of style atom -are the only ones that can be used with this fix since they produce -per-atom vectors. -

    -

    Each per-atom value of each input vector is averaged independently. -

    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used in order to contribute to the -average. The final averaged quantities are generated on timesteps -that are a multiple of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. -

    -
    - -

    The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are -self-explanatory. Note that other atom attributes can be used as -inputs to this fix by using the compute -property/atom command and then specifying -an input value from that compute. -

    -

    IMPORTANT NOTE: The x,y,z attributes are values that are re-wrapped -inside the periodic box whenever an atom crosses a periodic boundary. -Thus if you time average an atom that spends half its time on either -side of the periodic box, you will get a value in the middle of the -box. If this is not what you want, consider averaging unwrapped -coordinates, which can be provided by the compute -property/atom command via its xu,yu,zu -attributes. -

    -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the per-atom vector calculated by the compute is used. If a -bracketed term containing an index I is appended, the Ith column of -the per-atom array calculated by the compute is used. Users can also -write code for their own compute styles and add them to -LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the per-atom vector calculated by the fix is used. If a -bracketed term containing an index I is appended, the Ith column of -the per-atom array calculated by the fix is used. Note that some -fixes only produce their values on certain timesteps, which must be -compatible with Nevery, else an error will result. Users can also -write code for their own fix styles and add them to -LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script as an atom-style -variable Variables of style atom can reference -thermodynamic keywords, or invoke other computes, fixes, or variables -when they are evaluated, so this is a very general means of generating -per-atom quantities to time average. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global scalar or vector quantities are -stored by this fix for access by various output -commands. -

    -

    This fix produces a per-atom vector or array which can be accessed by -various output commands. A vector is -produced if only a single quantity is averaged by this fix. If two or -more quantities are averaged, then an array of values is produced. -The per-atom values can only be accessed on timesteps that are -multiples of Nfreq since that is when averaging is performed. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute, fix ave/histo, fix -ave/spatial, fix ave/time, -variable, -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_ave_chunk.html b/doc/doc2/fix_ave_chunk.html deleted file mode 100644 index 5440b74530..0000000000 --- a/doc/doc2/fix_ave_chunk.html +++ /dev/null @@ -1,464 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/chunk command -

    -

    Syntax: -

    -
    fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ave/chunk = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of times to use input values for calculating averages - -
    • Nfreq = calculate averages every this many timesteps - -
    • chunkID = ID of compute chunk/atom command - -
    • one or more input values can be listed - -
    • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name - -
        vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-  density/number, density/mass = number or mass density
-  temp = temperature
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = norm or ave or bias or adof or cdof or file or overwrite or title1 or title2 or title3 - -
        norm arg = all or sample or none = how output on Nfreq steps is normalized
-    all = output is sum of atoms across all Nrepeat samples, divided by atom count
-    sample = output is sum of Nrepeat sample averages, divided by Nrepeat
-    none = output is sum of Nrepeat sums, divided by Nrepeat
-  ave args = one or running or window M
-    one = output new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  bias arg = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
-  adof value = dof_per_atom
-    dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
-  cdof value = dof_per_chunk
-    dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
-  file arg = filename
-    filename = file to write results to
-  overwrite arg = none = overwrite output file with only latest output
-  format arg = string
-    string = C-style format string
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
-fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running 
-
    -

    IMPORTANT NOTE: -

    -

    If you are trying to replace an older fix ave/spatial command with the -newer, more flexible fix ave/chunk and compute -chunk/atom commands, you simply need to split -the fix ave/spatial arguments across the two new commands. For -example, this command: -

    -
    fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile 
-
    -

    could be replaced by: -

    -
    compute cc1 flow chunk/atom bin/1d y 0.0 1.0 
-fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile 
-
    -

    Description: -

    -

    Use one or more per-atom vectors as inputs every few timesteps, sum -the values over the atoms in each chunk at each timestep, then average -the per-chunk values over longer timescales. The resulting chunk -averages can be used by other output -commands such as thermo_style -custom, and can also be written to a file. -

    -

    In LAMMPS, chunks are collections of atoms defined by a compute -chunk/atom command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute -chunk/atom doc page and "Section_howto -23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. -

    -

    Note that only atoms in the specified group contribute to the summing -and averaging calculations. The compute -chunk/atom command defines its own group as -well as an optional region. Atoms will have a chunk ID = 0, meaning -they belong to no chunk, if they are not in that group or region. -Thus you can specify the "all" group for this command if you simply -want to use the chunk definitions provided by chunkID. -

    -

    Each specified per-atom value can be an atom attribute (position, -velocity, force component), a mass or number density, or the result of -a compute or fix or the evaluation of an -atom-style variable. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. Note that the compute -property/atom command provides access to -any attribute defined and stored by atoms. If you wish to -time-average global quantities from a compute, fix, or variable, then -see the fix ave/time command. -

    -

    Computes that produce per-atom quantities are those -which have the word atom in their style name. See the doc pages for -individual fixes to determine which ones produce per-atom -quantities. Variables of style atom are the only -ones that can be used with this fix since all other styles of variable -produce global quantities. -

    -

    The per-atom values of each input vector are summed and averaged -independently of the per-atom values in other input vectors. -

    -

    IMPORTANT NOTE: This fix works by creating an array of size Nchunk -by Nvalues on each processor. Nchunk is the number of chunks which -is defined by the compute chunk/atom -command. Nvalues is the number of input values specified. Each -processor loops over its atoms, tallying its values to the appropriate -chunk. Then the entire array is summed across all processors. This -means that using a large number of chunks will incur an overhead in -memory and computational cost (summing across processors), so be -careful to define a reasonable number of chunks. -

    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be accessed and contribute to the -average. The final averaged quantities are generated on timesteps -that are a multiples of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. -

    -

    Each input value can also be averaged over the atoms in each chunk. -The way the averaging is done across the Nrepeat timesteps to -produce output on the Nfreq timesteps, and across multiple Nfreq -outputs, is determined by the norm and ave keyword settings, as -discussed below. -

    -

    IMPORTANT NOTE: To perform per-chunk averaging within a Nfreq time -window, the number of chunks Nchunk defined by the compute -chunk/atom command must remain constant. If -the ave keyword is set to running or window then Nchunk must -remain constant for the duration of the simulation. This fix forces -the chunk/atom compute specified by chunkID to hold Nchunk constant -for the appropriate time windows, by not allowing it to re-calcualte -Nchunk, which can also affect how it assigns chunk IDs to atoms. -More details are given on the compute -chunk/atom doc page. -

    -
    - -

    The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -As noted above, any other atom attributes can be used as input values -to this fix by using the compute -property/atom command and then specifying -an input value from that compute. -

    -

    The density/number value means the number density is computed for -each chunk, i.e. number/volume. The density/mass value means the -mass density is computed for each chunk, i.e. total-mass/volume. The -output values are in units of 1/volume or density (mass/volume). See -the units command doc page for the definition of density -for each choice of units, e.g. gram/cm^3. If the chunks defined by -the compute chunk/atom command are spatial -bins, the volume is the bin volume. Otherwise it is the volume of the -entire simulation box. -

    -

    The temp value means the temperature is computed for each chunk, by -the formula KE = DOF/2 k T, where KE = total kinetic energy of the -chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees -of freedom for all atoms in the chunk, k = Boltzmann constant, and T = -temperature. -

    -

    The DOF is calculated as N*adof + cdof, where N = number of atoms in -the chunk, adof = degrees of freedom per atom, and cdof = degrees of -freedom per chunk. By default adof = 2 or 3 = dimensionality of -system, as set via the dimension command, and cdof = -0.0. This gives the usual formula for temperature. -

    -

    Note that currently this temperature only includes translational -degrees of freedom for each atom. No rotational degrees of freedom -are included for finite-size particles. Also no degrees of freedom -are subtracted for any velocity bias or constraints that are applied, -such as compute temp/partial, or fix -shake or fix rigid. This is because -those degrees of freedom (e.g. a constrained bond) could apply to sets -of atoms that are both included and excluded from a specific chunk, -and hence the concept is somewhat ill-defined. In some cases, you can -use the adof and cdof keywords to adjust the calculated degress of -freedom appropriately, as explained below. -

    -

    Also note that a bias can be subtracted from atom velocities before -they are used in the above formula for KE, by using the bias -keyword. This allows, for example, a thermal temperature to be -computed after removal of a flow velocity profile. -

    -

    Note that the per-chunk temperature calculated by this fix and the -compute temp/chunk command can be different. -The compute calculates the temperature for each chunk for a single -snapshot. This fix can do that but can also time average those values -over many snapshots, or it can compute a temperature as if the atoms -in the chunk on different timesteps were collected together as one set -of atoms to calculate their temperature. The compute allows the -center-of-mass velocity of each chunk to be subtracted before -calculating the temperature; this fix does not. -

    -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and add them to LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -Nevery, else an error results. Users can also write code for their -own fix styles and add them to LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables of style -atom can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to average within chunks. -

    -
    - -

    Additional optional keywords also affect the operation of this fix -and its outputs. -

    -

    The norm keyword affects how averaging is done for the per-chunk -values that are output every Nfreq timesteps. -

    -

    It the norm setting is all, which is the default, a chunk value is -summed over all atoms in all Nrepeat samples, as is the count of -atoms in the chunk. The averaged output value for the chunk on the -Nfreq timesteps is Total-sum / Total-count. In other words it is an -average over atoms across the entire Nfreq timescale. -

    -

    If the norm setting is sample, the chunk value is summed over atoms -for each sample, as is the count, and an "average sample value" is -computed for each sample, i.e. Sample-sum / Sample-count. The outuput -value for the chunk on the Nfreq timesteps is the average of the -Nrepeat "average sample values", i.e. the sum of Nrepeat "average -sample values" divided by Nrepeat. In other words it is an average -of an average. -

    -

    If the norm setting is none, a similar computation as for the -sample seting is done, except the individual "average sample values" -are "summed sample values". A summed sample value is simply the chunk -value summed over atoms in the sample, without dividing by the number -of atoms in the sample. The outuput value for the chunk on the -Nfreq timesteps is the average of the Nrepeat "summed sample -values", i.e. the sum of Nrepeat "summed sample values" divided by -Nrepeat. -

    -

    The ave keyword determines how the per-chunk values produced every -Nfreq steps are averaged with values produced on previous steps that -were multiples of Nfreq, before they are accessed by another output -command or written to a file. -

    -

    If the ave setting is one, which is the default, then the chunk -values produced on timesteps that are multiples of Nfreq are -independent of each other; they are output as-is without further -averaging. -

    -

    If the ave setting is running, then the chunk values produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cumulative sense before being output. Each output chunk value is thus -the average of the chunk value produced on that timestep with all -preceding values for the same chunk. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the unfix command, or re-defining the fix by -re-specifying it. -

    -

    If the ave setting is window, then the chunk values produced on -timesteps that are multiples of Nfreq are summed and averaged within -a moving "window" of time, so that the last M values for the same -chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000, -then the output on step 10000 will be the average of the individual -chunk values on steps 8000,9000,10000. Outputs on early steps will -average over less than M values if they are not available. -

    -

    The bias keyword specifies the ID of a temperature compute that -removes a "bias" velocity from each atom, specified as bias-ID. It -is only used when the temp value is calculated, to compute the -thermal temperature of each chunk after the translational kinetic -energy components have been altered in a prescribed way, e.g. to -remove a flow velocity profile. See the doc pages for individual -computes that calculate a temperature to see which ones implement a -bias. -

    -

    The adof and cdof keywords define the values used in the degree of -freedom (DOF) formula described above for for temperature calculation -for each chunk. They are only used when the temp value is -calculated. They can be used to calculate a more appropriate -temperature for some kinds of chunks. Here are 3 examples: -

    -

    If spatially binned chunks contain some number of water molecules and -fix shake is used to make each molecule rigid, then -you could calculate a temperature with 6 degrees of freedom (DOF) (3 -translational, 3 rotational) per molecule by setting adof to 2.0. -

    -

    If compute temp/partial is used with the -bias keyword to only allow the x component of velocity to contribute -to the temperature, then adof = 1.0 would be appropriate. -

    -

    If each chunk consists of a large molecule, with some number of its -bonds constrained by fix shake or the entire molecule -by fix rigid/small, adof = 0.0 and cdof could be -set to the remaining degrees of freedom for the entire molecule -(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid -molecule. -

    -

    The file keyword allows a filename to be specified. Every Nfreq -timesteps, a section of chunk info will be written to a text file in -the following format. A line with the timestep and number of chunks -is written. Then one line per chunk is written, containing the chunk -ID (1-Nchunk), an optional original ID value, optional coordinate -values for chunks that represent spatial bins, the number of atoms in -the chunk, and one or more calculated values. More explanation of the -optional values is given below. The number of values in each line -corresponds to the number of values specified in the fix ave/chunk -command. The number of atoms and the value(s) are summed or average -quantities, as explained above. -

    -

    The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting. -

    -

    The format keyword sets the numeric format of each value when it is -printed to a file via the file keyword. Note that all values are -floating point quantities. The default format is %g. You can specify -a higher precision if desired, e.g. %20.16g. -

    -

    The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the file keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. -

    -

    By default, these header lines are as follows: -

    -
    # Chunk-averaged data for fix ID and group name
-# Timestep Number-of-chunks
-# Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ... 
-
    -

    In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate value names, e.g. fx or c_myCompute2. -

    -

    The words in parenthesis only appear with corresponding columns if the -chunk style specified for the compute -chunk/atom command supports them. The OrigID -column is only used if the compress keyword was set to yes for the -compute chunk/atom command. This means that -the original chunk IDs (e.g. molecule IDs) will have been compressed -to remove chunk IDs with no atoms assigned to them. Thus a compresed -chunk ID of 3 may correspond to an original chunk ID or molecule ID of -415. The OrigID column will list 415 for the 3rd chunk. -

    -

    The CoordN columns only appear if a binning style was used in the -compute chunk/atom command. For bin/1d, -bin/2d, and bin/3d styles the column values are the center point -of the bin in the corresponding dimension. Just Coord1 is used for -bin/1d, Coord2 is added for bin/2d, Coord3 is added for bin/3d. -

    -

    Note that if the value of the units keyword used in the compute -chunk/atom command is box or lattice, the -coordinate values will be in distance units. If the -value of the units keyword is reduced, the coordinate values will -be in unitless reduced units (0-1). -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global array of values which can be accessed by -various output commands. The values can -only be accessed on timesteps that are multiples of Nfreq since that -is when averaging is performed. The global array has # of rows = -the number of chunks Nchunk as calculated by the specified compute -chunk/atom command. The # of columns = -M+1+Nvalues, where M = 1 to 4, depending on whether the optional -columns for OrigID and CoordN are used, as explained above. -Following the optional columns, the next column contains the count of -atoms in the chunk, and the remaining columns are the Nvalue -quantities. When the array is accessed with a row I that exceeds the -current number of chunks, than a 0.0 is returned by the fix instead of -an error, since the number of chunks can vary as a simulation runs -depending on how that value is computed by the compute chunk/atom -command. -

    -

    The array values calculated by this fix are treated as "intensive", -since they are typically already normalized by the count of atoms in -each chunk. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute, fix ave/atom, fix -ave/histo, fix ave/time, -variable, fix ave/correlate -

    -

    Default: -

    -

    The option defaults are norm = all, ave = one, bias = none, no file output, and -title 1,2,3 = strings as described above. -

    - diff --git a/doc/doc2/fix_ave_correlate.html b/doc/doc2/fix_ave_correlate.html deleted file mode 100644 index 860459bdb4..0000000000 --- a/doc/doc2/fix_ave_correlate.html +++ /dev/null @@ -1,353 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/correlate command -

    -

    Syntax: -

    -
    fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ave/correlate = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of correlation time windows to accumulate - -
    • Nfreq = calculate time window averages every this many timesteps - -
    • one or more input values can be listed - -
    • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name - -
        c_ID = global scalar calculated by a compute with ID
-  c_ID[I] = Ith component of global vector calculated by a compute with ID
-  f_ID = global scalar calculated by a fix with ID
-  f_ID[I] = Ith component of global vector calculated by a fix with ID
-  v_name = global value calculated by an equal-style variable with name 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = type or ave or start or prefactor or file or overwrite or title1 or title2 or title3 - -
        type arg = auto or upper or lower or auto/upper or auto/lower or full
-    auto = correlate each value with itself
-    upper = correlate each value with each succeeding value
-    lower = correlate each value with each preceding value
-    auto/upper = auto + upper
-    auto/lower = auto + lower
-    full = correlate each value with every other value, including itself = auto + upper + lower
-  ave args = one or running
-    one = zero the correlation accumulation every Nfreq steps
-    running = accumulate correlations continuously
-  start args = Nstart
-    Nstart = start accumulating correlations on this timestep
-  prefactor args = value
-    value = prefactor to scale all the correlation data by
-  file arg = filename
-    filename = name of file to output correlation data to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
-fix 1 all ave/correlate 1 50 10000 &
-          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
-	  type upper ave running title1 "My correlation data" 
-
    -

    Description: -

    -

    Use one or more global scalar values as inputs every few timesteps, -calculate time correlations bewteen them at varying time intervals, -and average the correlation data over longer timescales. The -resulting correlation values can be time integrated by -variables or used by other output -commands such as thermo_style -custom, and can also be written to a file. See the -fix ave/correlate/long command for an -alternate method for computing correlation functions efficiently over -very long time windows. -

    -

    The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. -

    -

    Each listed value can be the result of a compute or -fix or the evaluation of an equal-style -variable. In each case, the compute, fix, or variable -must produce a global quantity, not a per-atom or local quantity. If -you wish to spatial- or time-average or histogram per-atom quantities -from a compute, fix, or variable, then see the fix -ave/spatial, fix ave/atom, -or fix ave/histo commands. If you wish to sum a -per-atom quantity into a single global quantity, see the compute -reduce command. -

    -

    Computes that produce global quantities are those which -do not have the word atom in their style name. Only a few -fixes produce global quantities. See the doc pages for -individual fixes for info on which ones produce such values. -Variables of style equal are the only ones that can -be used with this fix. Variables of style atom cannot be used, -since they produce per-atom values. -

    -

    The input values must either be all scalars. What kinds of -correlations between input values are calculated is determined by the -type keyword as discussed below. -

    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used to calculate correlation data. -The input values are sampled every Nevery timesteps. The -correlation data for the preceding samples is computed on timesteps -that are a multiple of Nfreq. Consider a set of samples from some -initial time up to an output timestep. The initial time could be the -beginning of the simulation or the last output time; see the ave -keyword for options. For the set of samples, the correlation value -Cij is calculated as: -

    -
    Cij(delta) = ave(Vi(t)*Vj(t+delta)) 
-
    -

    which is the correlation value between input values Vi and Vj, -separated by time delta. Note that the second value Vj in the pair is -always the one sampled at the later time. The ave() represents an -average over every pair of samples in the set that are separated by -time delta. The maximum delta used is of size (Nrepeat-1)*Nevery. -Thus the correlation between a pair of input values yields Nrepeat -correlation datums: -

    -
    Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery) 
-
    -

    For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on -timesteps 0,5,10,15,...,100 will be used to compute the final averages -on timestep 100. Six averages will be computed: Cij(0), Cij(5), -Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will -be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15), -Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100). -

    -

    Nfreq must be a multiple of Nevery; Nevery and Nrepeat must be -non-zero. Also, if the ave keyword is set to one which is the -default, then Nfreq >= (Nrepeat-1)*Nevery is required. -

    -
    - -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the compute is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the compute is used. -

    -

    Note that there is a compute reduce command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix ave/correlate. Or it can be a compute -defined not in your input script, but by thermodynamic -output or other fixes such as fix nvt -or fix temp/rescale. See the doc pages for -these commands which give the IDs of these computes. Users can also -write code for their own compute styles and add them to -LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the fix is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the fix is used. -

    -

    Note that some fixes only produce their values on certain timesteps, -which must be compatible with Nevery, else an error will result. -Users can also write code for their own fix styles and add them to -LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Only equal-style -variables can be referenced. See the variable command -for details. Note that variables of style equal define a formula -which can reference individual atom properties or thermodynamic -keywords, or they can invoke other computes, fixes, or variables when -they are evaluated, so this is a very general means of specifying -quantities to time correlate. -

    -
    - -

    Additional optional keywords also affect the operation of this fix. -

    -

    The type keyword determines which pairs of input values are -correlated with each other. For N input values Vi, for i = 1 to N, -let the number of pairs = Npair. Note that the second value in the -pair Vi(t)*Vj(t+delta) is always the one sampled at the later time. -

    -
    • If type is set to auto then each input value is correlated with -itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N. - -
    • If type is set -to upper then each input value is correlated with every succeeding -value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. - -
    • If type is set -to lower then each input value is correlated with every preceeding -value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. - -
    • If type is set to auto/upper then each input value is correlated -with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j, -so Npair = N*(N+1)/2. - -
    • If type is set to auto/lower then each input value is correlated -with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j, -so Npair = N*(N+1)/2. - -
    • If type is set to full then each input value is correlated with -itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so -Npair = N^2. -
    -

    The ave keyword determines what happens to the accumulation of -correlation samples every Nfreq timesteps. If the ave setting is -one, then the accumulation is restarted or zeroed every Nfreq -timesteps. Thus the outputs on successive Nfreq timesteps are -essentially independent of each other. The exception is that the -Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of -Nfreq, contributes to the correlation output both at time T and at -time T+Nfreq. -

    -

    If the ave setting is running, then the accumulation is never -zeroed. Thus the output of correlation data at any timestep is the -average over samples accumulated every Nevery steps since the fix -was defined. it can only be restarted by deleting the fix via the -unfix command, or by re-defining the fix by re-specifying -it. -

    -

    The start keyword specifies what timestep the accumulation of -correlation samples will begin on. The default is step 0. Setting it -to a larger value can avoid adding non-equilibrated data to the -correlation averages. -

    -

    The prefactor keyword specifies a constant which will be used as a -multiplier on the correlation data after it is averaged. It is -effectively a scale factor on Vi*Vj, which can be used to account for -the size of the time window or other unit conversions. -

    -

    The file keyword allows a filename to be specified. Every Nfreq -steps, an array of correlation data is written to the file. The -number of rows is Nrepeat, as described above. The number of -columns is the Npair+2, also as described above. Thus the file ends -up to be a series of these array sections. -

    -

    The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting. -

    -

    The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the file keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. -

    -

    By default, these header lines are as follows: -

    -
    # Time-correlated data for fix ID
-# TimeStep Number-of-time-windows
-# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ... 
-
    -

    In the first line, ID is replaced with the fix-ID. The second line -describes the two values that are printed at the first of each section -of output. In the third line the value pairs are replaced with the -appropriate fields from the fix ave/correlate command. -

    -
    - -

    Let Sij = a set of time correlation data for input values I and J, -namely the Nrepeat values: -

    -
    Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery) 
-
    -

    As explained below, these datums are output as one column of a global -array, which is effectively the correlation matrix. -

    -

    The trap function defined for equal-style variables -can be used to perform a time integration of this vector of datums, -using a trapezoidal rule. This is useful for calculating various -quantities which can be derived from time correlation data. If a -normalization factor is needed for the time integration, it can be -included in the variable formula or via the prefactor keyword. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global array of values which can be accessed by -various output commands. The values can -only be accessed on timesteps that are multiples of Nfreq since that -is when averaging is performed. The global array has # of rows = -Nrepeat and # of columns = Npair+2. The first column has the time -delta (in timesteps) between the pairs of input values used to -calculate the correlation, as described above. The 2nd column has the -number of samples contributing to the correlation average, as -described above. The remaining Npair columns are for I,J pairs of the -N input values, as determined by the type keyword, as described -above. -

    -
    • For type = auto, the Npair = N columns are ordered: C11, C22, ..., -CNN. - -
    • For type = upper, the Npair = N*(N-1)/2 columns are ordered: C12, -C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N. - -
    • For type = lower, the Npair = N*(N-1)/2 columns are ordered: C21, -C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1. - -
    • For type = auto/upper, the Npair = N*(N+1)/2 columns are ordered: -C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N, -CNN. - -
    • For type = auto/lower, the Npair = N*(N+1)/2 columns are ordered: -C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1, -CNN. - -
    • For type = full, the Npair = N^2 columns are ordered: C11, C12, -..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, -CNN. -
    -

    The array values calculated by this fix are treated as "intensive". -If you need to divide them by the number of atoms, you must do this in -a later processing step, e.g. when using them in a -variable. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix ave/correlate/long, -compute, fix ave/time, fix -ave/atom, fix ave/spatial, -fix ave/histo, variable -

    -

    Default: none -

    -

    The option defaults are ave = one, type = auto, start = 0, no file -output, title 1,2,3 = strings as described above, and prefactor = 1.0. -

    - diff --git a/doc/doc2/fix_ave_correlate_long.html b/doc/doc2/fix_ave_correlate_long.html deleted file mode 100644 index 05f4526650..0000000000 --- a/doc/doc2/fix_ave_correlate_long.html +++ /dev/null @@ -1,159 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/correlate/long command -

    -

    Syntax: -

    -
    fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ave/correlate/long = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nfreq = save state of the time correlation functions every this many timesteps - -
    • one or more input values can be listed - -
    • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name - -
        c_ID = global scalar calculated by a compute with ID
-  c_ID[I] = Ith component of global vector calculated by a compute with ID
-  f_ID = global scalar calculated by a fix with ID
-  f_ID[I] = Ith component of global vector calculated by a fix with ID
-  v_name = global value calculated by an equal-style variable with name 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = type or start or file or overwrite or title1 or title2 or ncorr or p or m - -
        type arg = auto or upper or lower or auto/upper or auto/lower or full
-    auto = correlate each value with itself
-    upper = correlate each value with each succeeding value
-    lower = correlate each value with each preceding value
-    auto/upper = auto + upper
-    auto/lower = auto + lower
-    full = correlate each value with every other value, including itself = auto + upper + lower
-  start args = Nstart
-    Nstart = start accumulating correlations on this timestep
-  file arg = filename
-    filename = name of file to output correlation data to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  ncorr arg = Ncorrelators
-    Ncorrelators = number of correlators to store
-  nlen args = Nlen
-    Nlen = length of each correlator
-  ncount args = Ncount
-    Ncount = number of values over which succesive correlators are averaged 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
-fix 1 all ave/correlate/long 1 10000 &
-          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
-	  type upper title1 "My correlation data" nlen 15 ncount 3 
-
    -

    Description: -

    -

    This fix is similar in spirit and syntax to the fix -ave/correlate. However, this fix allows the -efficient calculation of time correlation functions on the fly over -extremely long time windows without too much CPU overhead, using a -multiple-tau method (Ramirez) that decreases the resolution -of the stored correlation function with time. -

    -

    The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. -

    -

    Each listed value can be the result of a compute or fix or the -evaluation of an equal-style variable. See the fix -ave/correlate doc page for details. -

    -

    The Nevery and Nfreq arguments specify on what timesteps the input -values will be used to calculate correlation data, and the frequency -with which the time correlation functions will be output to a file. -Note that there is no Nrepeat argument, unlike the fix -ave/correlate command. -

    -

    The optional keywords ncorr, nlen, and ncount are unique to this -command and determine the number of correlation points calculated and -the memory and CPU overhead used by this calculation. Nlen and -ncount determine the amount of averaging done at longer correlation -times. The default values nlen=16, ncount=2 ensure that the -systematic error of the multiple-tau correlator is always below the -level of the statistical error of a typical simulation (which depends -on the ensemble size and the simulation length). -

    -

    The maximum correlation time (in time steps) that can be reached is -given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation -times are discarded and not calculated. With the default values of -the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to -7864320 time steps. If longer correlation times are needed, the value -of ncorr should be increased. Using nlen=16 and ncount=2, with -ncorr=30, the maximum number of steps that can be correlated is -80530636808. If ncorr=40, correlation times in excess of 8e12 time -steps can be calculated. -

    -

    The total memory needed for each correlation pair is roughly -4*ncorr*nlen*8 bytes. With the default values of the parameters, this -corresponds to about 10 KB. -

    -

    For the meaning of the additional optional keywords, see the fix -ave/correlate doc page. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Since this fix in intended for the calculation of time correlation -functions over very long MD simulations, the information about this -fix is written automatically to binary restart files, so that the time -correlation calculation can continue in subsequent simulations. None -of the fix_modify options are relevant to this fix. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix ave/correlate -

    -

    Default: none -

    -

    The option defaults for keywords that are also keywords for the fix -ave/correlate command are as follows: type = -auto, start = 0, no file output, title 1,2 = strings as described on -the fix ave/correlate doc page. -

    -

    The option defaults for keywords unique to this command are as -follows: ncorr=20, nlen=16, ncount=2. -

    -
    - - - -

    (Ramirez) J. Ramirez, S.K. Sukumaran, B. Vorselaars and -A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010). -

    - diff --git a/doc/doc2/fix_ave_histo.html b/doc/doc2/fix_ave_histo.html deleted file mode 100644 index 7fd6291e6d..0000000000 --- a/doc/doc2/fix_ave_histo.html +++ /dev/null @@ -1,351 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/histo command -

    -

    fix ave/histo/weight command -

    -

    Syntax: -

    -
    fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • style = ave/histo or ave/histo/weight = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of times to use input values for calculating histogram - -
    • Nfreq = calculate histogram every this many timesteps - -
    • lo,hi = lo/hi bounds within which to histogram - -
    • Nbin = # of histogram bins - -
    • one or more input values can be listed - -
    • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name - -
        x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = scalar or vector calculated by a compute with ID
-  c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
-  f_ID = scalar or vector calculated by a fix with ID
-  f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
-  v_name = value(s) calculated by an equal-style or atom-style variable with name 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = mode or file or ave or start or beyond or overwrite or title1 or title2 or title3 - -
        mode arg = scalar or vector
-    scalar = all input values are scalars
-    vector = all input values are vectors
-  file arg = filename
-    filename = name of file to output histogram(s) to
-  ave args = one or running or window
-    one = output a new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  start args = Nstart
-    Nstart = start averaging on this timestep
-  beyond arg = ignore or end or extra
-    ignore = ignore values outside histogram lo/hi bounds
-    end = count values outside histogram lo/hi bounds in end bins
-    extra = create 2 extra bins for value outside histogram lo/hi bounds
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file, only for vector mode 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
-fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
-fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra 
-fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2] 
-
    -

    Description: -

    -

    Use one or more values as inputs every few timesteps, histogram them, -and average the histogram over longer timescales. The resulting -histogram can be used by other output -commands, and can also be written to a -file. The fix ave/histo/weight command has identical syntax to fix -ave/histo, except that exactly two values must be specified. See -details below. -

    -

    The group specified with this command is ignored for global and local -input values. For per-atom input values, only atoms in the group -contribute to the histogram. Note that regardless of the specified -group, specified values may represent calculations performed by -computes and fixes which store their own "group" definition. -

    -

    A histogram is simply a count of the number of values that fall within -a histogram bin. Nbins are defined, with even spacing between lo -and hi. Values that fall outside the lo/hi bounds can be treated in -different ways; see the discussion of the beyond keyword below. -

    -

    Each input value can be an atom attribute (position, velocity, force -component) or can be the result of a compute or -fix or the evaluation of an equal-style or atom-style -variable. The set of input values can be either all -global, all per-atom, or all local quantities. Inputs of different -kinds (e.g. global and per-atom) cannot be mixed. Atom attributes are -per-atom vector values. See the doc page for individual "compute" and -"fix" commands to see what kinds of quantities they generate. -

    -

    The input values must either be all scalars or all vectors (or -arrays), depending on the setting of the mode keyword. -

    -

    Note that the output of this command is a single histogram for all -input values combined together, not one histogram per input value. -See below for details on the format of the output of this fix. -

    -

    If mode = vector, then the input values may either be vectors or -arrays. If a global array is listed, then it is the same as if the -individual columns of the array had been listed one by one. -E.g. these 2 fix ave/histo commands are equivalent, since the compute -com/chunk command creates a global array -with 3 columns: -

    -
    compute myCOM all com/chunk
-fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
-fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector 
-
    -

    If the fix ave/histo/weight command is used, exactly two values must -be specified. If the values are vectors, they must be the same -length. The first value (a scalar or vector) is what is histogrammed -into bins, in the same manner the fix ave/histo command operates. The -second value (a scalar or vector) is used as a "weight". This means -that instead of each value tallying a "1" to its bin, the -corresponding weight is tallied. E.g. the Nth entry in the first -vector tallies the Nth entry (weight) in the second vector. -

    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used in order to contribute to the -histogram. The final histogram is generated on timesteps that are -multiple of Nfreq. It is averaged over Nrepeat histograms, -computed in the preceding portion of the simulation every Nevery -timesteps. Nfreq must be a multiple of Nevery and Nevery must -be non-zero even if Nrepeat is 1. Also, the timesteps -contributing to the histogram value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values -on timesteps 90,92,94,96,98,100 will be used to compute the final -histogram on timestep 100. Similarly for timesteps -190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq -= 100, then no time averaging of the histogram is done; a histogram is -simply generated on timesteps 100,200,etc. -

    -
    - -

    The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are -self-explanatory. Note that other atom attributes can be used as -inputs to this fix by using the compute -property/atom command and then specifying -an input value from that compute. -

    -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If mode = scalar, then if -no bracketed term is appended, the global scalar calculated by the -compute is used. If a bracketed term is appended, the Ith element of -the global vector calculated by the compute is used. If mode = -vector, then if no bracketed term is appended, the global or per-atom -or local vector calculated by the compute is used. Or if the compute -calculates an array, all of the columns of the array are used as if -they had been specified as individual vectors (see description above). -If a bracketed term is appended, the Ith column of the global or -per-atom or local array calculated by the compute is used. -

    -

    Note that there is a compute reduce command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix ave/histo. Or it can be a compute defined -not in your input script, but by thermodynamic -output or other fixes such as fix -nvt or fix temp/rescale. See -the doc pages for these commands which give the IDs of these computes. -Users can also write code for their own compute styles and add them -to LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If mode = scalar, then if -no bracketed term is appended, the global scalar calculated by the fix -is used. If a bracketed term is appended, the Ith element of the -global vector calculated by the fix is used. If mode = vector, then -if no bracketed term is appended, the global or per-atom or local -vector calculated by the fix is used. Or if the fix calculates an -array, all of the columns of the array are used as if they had been -specified as individual vectors (see description above). If a -bracketed term is appended, the Ith column of the global or per-atom -or local array calculated by the fix is used. -

    -

    Note that some fixes only produce their values on certain timesteps, -which must be compatible with Nevery, else an error will result. -Users can also write code for their own fix styles and add them to -LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. If mode = scalar, then -only equal-style variables can be used, which produce a global value. -If mode = vector, then only atom-style variables can be used, which -produce a per-atom vector. See the variable command -for details. Note that variables of style equal and atom define a -formula which can reference individual atom properties or -thermodynamic keywords, or they can invoke other computes, fixes, or -variables when they are evaluated, so this is a very general means of -specifying quantities to histogram. -

    -
    - -

    Additional optional keywords also affect the operation of this fix. -

    -

    If the mode keyword is set to scalar, then all input values must -be global scalars, or elements of global vectors. If the mode -keyword is set to vector, then all input values must be global or -per-atom or local vectors, or columns of global or per-atom or local -arrays. -

    -

    The beyond keyword determines how input values that fall outside the -lo to hi bounds are treated. Values such that lo <= value <= -hi are assigned to one bin. Values on a bin boundary are assigned -to the lower of the 2 bins. If beyond is set to ignore then -values < lo and values > hi are ignored, i.e. they are not binned. -If beyond is set to end then values < lo are counted in the -first bin and values > hi are counted in the last bin. If beyond -is set to extend then two extra bins are created, so that there are -Nbins+2 total bins. Values < lo are counted in the first bin and -values > hi are counted in the last bin (Nbins+1). Values between -lo and hi (inclusive) are counted in bins 2 thru Nbins+1. The -"coordinate" stored and printed for these two extra bins is lo and -hi. -

    -

    The ave keyword determines how the histogram produced every Nfreq -steps are averaged with histograms produced on previous steps that -were multiples of Nfreq, before they are accessed by another output -command or written to a file. -

    -

    If the ave setting is one, then the histograms produced on -timesteps that are multiples of Nfreq are independent of each other; -they are output as-is without further averaging. -

    -

    If the ave setting is running, then the histograms produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cumulative sense before being output. Each bin value in the histogram -is thus the average of the bin value produced on that timestep with -all preceding values for the same bin. This running average begins -when the fix is defined; it can only be restarted by deleting the fix -via the unfix command, or by re-defining the fix by -re-specifying it. -

    -

    If the ave setting is window, then the histograms produced on -timesteps that are multiples of Nfreq are summed within a moving -"window" of time, so that the last M histograms are used to produce -the output. E.g. if M = 3 and Nfreq = 1000, then the output on step -10000 will be the combined histogram of the individual histograms on -steps 8000,9000,10000. Outputs on early steps will be sums over less -than M histograms if they are not available. -

    -

    The start keyword specifies what timestep histogramming will begin -on. The default is step 0. Often input values can be 0.0 at time 0, -so setting start to a larger value can avoid including a 0.0 in -a running or windowed histogram. -

    -

    The file keyword allows a filename to be specified. Every Nfreq -steps, one histogram is written to the file. This includes a leading -line that contains the timestep, number of bins, the total count of -values contributing to the histogram, the count of values that were -not histogrammed (see the beyond keyword), the minimum value -encountered, and the maximum value encountered. The min/max values -include values that were not histogrammed. Following the leading -line, one line per bin is written into the file. Each line contains -the bin #, the coordinate for the center of the bin (between lo and -hi), the count of values in the bin, and the normalized count. The -normalized count is the bin count divided by the total count (not -including values not histogrammed), so that the normalized values sum -to 1.0 across all bins. -

    -

    The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting. -

    -

    The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the file keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. -

    -

    By default, these header lines are as follows: -

    -
    # Histogram for fix ID
-# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
-# Bin Coord Count Count/Total 
-
    -

    In the first line, ID is replaced with the fix-ID. The second line -describes the six values that are printed at the first of each section -of output. The third describes the 4 values printed for each bin in -the histogram. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix produces a global vector and global array which can be -accessed by various output commands. -The values can only be accessed on timesteps that are multiples of -Nfreq since that is when a histogram is generated. The global -vector has 4 values: -

    -
    • 1 = total counts in the histogram -
    • 2 = values that were not histogrammed (see beyond keyword) -
    • 3 = min value of all input values, including ones not histogrammed -
    • 4 = max value of all input values, including ones not histogrammed -
    -

    The global array has # of rows = Nbins and # of columns = 3. The -first column has the bin coordinate, the 2nd column has the count of -values in that histogram bin, and the 3rd column has the bin count -divided by the total count (not including missing counts), so that the -values in the 3rd column sum to 1.0. -

    -

    The vector and array values calculated by this fix are all treated as -"intensive". If this is not the case, e.g. due to histogramming -per-atom input values, then you will need to account for that when -interpreting the values produced by this fix. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute, fix ave/atom, fix -ave/spatial, fix ave/time, -variable, fix ave/correlate, -

    -

    Default: none -

    -

    The option defaults are mode = scalar, ave = one, start = 0, no file -output, beyond = ignore, and title 1,2,3 = strings as described above. -

    - diff --git a/doc/doc2/fix_ave_spatial.html b/doc/doc2/fix_ave_spatial.html deleted file mode 100644 index 747ca62946..0000000000 --- a/doc/doc2/fix_ave_spatial.html +++ /dev/null @@ -1,435 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/spatial command -

    -

    Syntax: -

    -
    fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ave/spatial = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of times to use input values for calculating averages - -
    • Nfreq = calculate averages every this many timesteps - -
    • dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins - -
        dim = x or y or z
-  origin = lower or center or upper or coordinate value (distance units)
-  delta = thickness of spatial bins in dim (distance units) 
-
      -
    • one or more input values can be listed - -
    • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name - -
        vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-  density/number, density/mass = number or mass density
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = region or bound or discard or norm or ave or units or file or overwrite or title1 or title2 or title3 - -
        region arg = region-ID
-  bound args = x/y/z lo hi
-    x/y/z = x or y or z to bound bins in this dimension
-    lo = lower or coordinate value (distance units)
-    hi = upper or coordinate value (distance units)
-  discard arg = mixed or no or yes
-    mixed = discard atoms outside bins only if bin bounds are explicitly set
-    no = always keep out-of-bounds atoms
-    yes = always discard out-of-bounds atoms
-  norm arg = all or sample
-    region-ID = ID of region atoms must be in to contribute to spatial averaging
-  ave args = one or running or window M
-    one = output new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  units arg = box or lattice or reduced
-  file arg = filename
-    filename = file to write results to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced &
-                      title1 "My output values"
-fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
-fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running
-fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running 
-
    -

    IMPORTANT NOTE: -

    -

    The fix ave/spatial command has been replaced by the more flexible -fix ave/chunk and compute -chunk/atom commands. The fix ave/spatial -command will be removed from LAMMPS sometime in the summer of 2015. -

    -

    Any fix ave/spatial command can be replaced by the two new commands. -You simply need to split the fix ave/spatial arguments across the two -new commands. For example, this command: -

    -
    fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile 
-
    -

    could be replaced by: -

    -
    compute cc1 flow chunk/atom bin/1d y 0.0 1.0 
-fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile 
-
    -

    Description: -

    -

    Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into 1d, 2d, or 3d bins based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other output -commands such as thermo_style -custom, and can also be written to a file. -

    -

    The group specified with the command means only atoms within the group -contribute to bin averages. If the region keyword is used, the atom -must be in both the specified group and the specified geometric -region in order to contribute to bin averages. -

    -

    Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -compute or fix or the evaluation of an -atom-style variable. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the fix -ave/time command. -

    -

    Computes that produce per-atom quantities are those -which have the word atom in their style name. See the doc pages for -individual fixes to determine which ones produce per-atom -quantities. Variables of style atom are the only -ones that can be used with this fix since all other styles of variable -produce global quantities. -

    -

    The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors. -

    -

    The size and dimensionality of the bins (1d = layers or slabs, 2d = -pencils, 3d = boxes) are determined by the dim, origin, and -delta settings and how many times they are specified (1, 2, or 3). -See details below. -

    -

    IMPORTANT NOTE: This fix works by creating an array of size Nbins by -Nvalues on each processor. Nbins is the total number of bins; Nvalues -is the number of input values specified. Each processor loops over -its atoms, tallying its values to the appropriate bin. Then the -entire array is summed across all processors. This means that using a -large number of bins (easy to do for 2d or 3d bins) will incur an -overhead in memory and computational cost (summing across processors), -so be careful to use reasonable numbers of bins. -

    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. -

    -
    - -

    Each per-atom property is also averaged over atoms in each bin. The -way the averaging is one across the Nrepeat timesteps to produce -output on the Nfreq timesteps, and across multiple Nfreq outputs, -is determined by the norm and av keyword settings, as discussed -below. -

    -

    Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends -on how many times (1, 2, or 3) the dim, origin, and delta -settings are specified in the fix ave/spatial command. For 2d or 3d -bins, there is no restriction on specifying dim = x before dim = y, or -dim = y before dim = z. Bins in a particular dim have a bin size in -that dimension given by delta. Every Nfreq steps, when averaging is -being performed and the per-atom property is calculated for the first -time, the number of bins and the bin sizes and boundaries are -computed. Thus if the simulation box changes size during a -simulation, the number of bins and their boundaries may also change. -In each dimension, bins are defined relative to a specified origin, -which may be the lower/upper edge of the simulation box in that -dimension, or its center point, or a specified coordinate value. -Starting at the origin, sufficient bins are created in both directions -to completely span the bin extent in that dimension. By default the -bin extent is the entire simulation box. -

    -

    The bound keyword can be used one or more times to limit the extent -of bin coverage in specified dimensions, i.e. to only bin a portion of -the box. If the lo setting is lower or the hi setting is -upper, the bin extent in that direction extends to the box boundary. -If a numeric value is used for lo and/or hi, then the bin extent -in the lo or hi direction extends only to that value, which is -assumed to be inside (or at least near) the simulation box boundaries, -though LAMMPS does not check for this. -

    -

    On each sampling timestep, each atom is mapped to the bin it currently -belongs to, based on its current position. Note that the group-ID and -region keyword can exclude specific atoms from this operation, as -discussed above. Note that between reneighboring timesteps, atoms can -move outside the current simulation box. If the box is periodic (in -that dimension) the atom is remapping into the periodic box for -purposes of binning. If the box in not periodic, the atom may have -moved outside the bounds of any bin. -

    -

    The discard keyword determines what is done with any atom which is -outside the bounds of any bin. If discard is set to yes, the atom -will be ignored and not contribute to any bin averages. If discard -is set to no, the atom will be counted as if it were in the first or -last bin in that dimension. If (discard is set to mixed, which is -the default, it will only be counted in the first or last bin if bins -extend to the box boundary in that dimension. This is the case if the -bound keyword settings are lower and upper, which is the -default. If the bound keyword settings are numeric values, then the -atom will be ignored if it is outside the bounds of any bin. Note -that in this case, it is possible that the first or last bin extends -beyond the numeric bounds settings, depending on the specified -origin. If this is the case, the atom is only ignored if it is -outside the first or last bin, not if it is simply outside the numeric -bounds setting. -

    -

    For orthogonal simulation boxes, the bins are also layers, pencils, or -boxes aligned with the xyz coordinate axes. For triclinic -(non-orthogonal) simulation boxes, the bins are so that they are -parallel to the tilted faces of the simulation box. See this -section of the manual for a discussion of -the geometry of triclinic boxes in LAMMPS. As described there, a -tilted simulation box has edge vectors a,b,c. In that nomenclature, -bins in the x dimension have faces with normals in the "b" cross "c" -direction. Bins in y have faces normal to the "a" cross "c" -direction. And bins in z have faces normal to the "a" cross "b" -direction. Note that in order to define the size and position of -these bins in an unambiguous fashion, the units option must be set -to reduced when using a triclinic simulation box, as noted below. -

    -
    - -

    The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the compute -property/atom command and then specifying -an input value from that compute. -

    -

    The density/number value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The density/mass -value means the mass density is computed in each bind, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the units command doc page for the -definition of density for each choice of units, e.g. gram/cm^3. -

    -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and add them to LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -Nevery, else an error results. Users can also write code for their -own fix styles and add them to LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables of style -atom can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average. -

    -
    - -

    Additional optional keywords also affect the operation of this fix. -The region, bound, and discard keywords were discussed above. -

    -

    The norm keyword affects how averaging is done for the output -produced every Nfreq timesteps. For an all setting, a bin -quantity is summed over all atoms in all Nrepeat samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire Nfreq timescale. -

    -

    For a sample setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a "average sample value" is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the Nrepeat "average sample values", In -other words it is an average of an average. -

    -

    The ave keyword determines how the bin values produced every Nfreq -steps are averaged with bin values produced on previous steps that -were multiples of Nfreq, before they are accessed by another output -command or written to a file. -

    -

    If the ave setting is one, then the bin values produced on -timesteps that are multiples of Nfreq are independent of each other; -they are output as-is without further averaging. -

    -

    If the ave setting is running, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the unfix command, or re-defining the fix by -re-specifying it. -

    -

    If the ave setting is window, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged within -a moving "window" of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available. -

    -

    The units keyword determines the meaning of the distance units used -for the bin size delta and for origin and bounds values if they -are coordinate value. For orthogonal simulation boxes, any of the 3 -options may be used. For non-orthogonal (triclinic) simulation boxes, -only the reduced option may be used. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacing. A reduced value means normalized -unitless values between 0 and 1, which represent the lower and upper -faces of the simulation box respectively. Thus an origin value of -0.5 means the center of the box in any dimension. A delta value of -0.1 means 10 bins span the box in that dimension. -

    -

    Consider a non-orthogonal box, with bins that are 1d layers or slabs -in the x dimension. No matter how the box is tilted, an origin of -0.0 means start layers at the lower "b" cross "c" plane of the -simulation box and an origin of 1.0 means to start layers at the -upper "b" cross "c" face of the box. A delta value of 0.1 means -there will be 10 layers from 0.0 to 1.0, regardless of the current -size or shape of the simulation box. -

    -

    The file keyword allows a filename to be specified. Every Nfreq -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms -in the bin, and one or more calculated values. The number of values -in each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the units keyword is box or -lattice, the "coord" is printed in box units. If the value of the -units keyword is reduced, the "coord" is printed in reduced units -(0-1). -

    -

    The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting. -

    -

    The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the file keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. -

    -

    By default, these header lines are as follows: -

    -
    # Spatial-averaged data for fix ID and group name
-# Timestep Number-of-bins
-# Bin Coord1 Coord2 Coord3 Count value1 value2 ... 
-
    -

    In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global array of values which can be accessed by -various output commands. The values can -only be accessed on timesteps that are multiples of Nfreq since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for -1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates -(center of the bin) in the appropriate dimensions, the next column has -the count of atoms in that bin, and the remaining columns are the -Nvalue quantities. When the array is accessed with an I that exceeds -the current number of bins, than a 0.0 is returned by the fix instead -of an error, since the number of bins can vary as a simulation runs, -depending on the simulation box size. 2d or 3d bins are ordered so -that the last dimension(s) vary fastest. The array values calculated -by this fix are "intensive", since they are already normalized by the -count of atoms in each bin. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    When the ave keyword is set to running or window then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn't change or if the units keyword is set to -reduced. -

    -

    Related commands: -

    -

    compute, fix ave/atom, fix -ave/histo, fix ave/time, -variable, fix ave/correlate, -fix ave/spatial/sphere -

    -

    Default: -

    -

    The option defaults are bound = lower and upper in all dimensions, -discard = mixed, norm = all, ave = one, units = lattice, no file -output, and title 1,2,3 = strings as described above. -

    - diff --git a/doc/doc2/fix_ave_spatial_sphere.html b/doc/doc2/fix_ave_spatial_sphere.html deleted file mode 100644 index 671c48318a..0000000000 --- a/doc/doc2/fix_ave_spatial_sphere.html +++ /dev/null @@ -1,343 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/spatial/sphere command -

    -

    Syntax: -

    -
    fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins value1 value2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ave/spatial = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of times to use input values for calculating averages - -
    • Nfreq = calculate averages every this many timesteps - -
    • origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below) - -
    • r_min = radial distance at which binning begins - -
    • r_max = radial distance at which binning ends - -
    • nbins = number of spherical shells to create between r_min and r_max - -
    • one or more input values can be listed - -
    • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name - -
        vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-  density/number, density/mass = number or mass density
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = region or norm or units or ave or file or overwrite or title1 or title2 or title3 - -
        region arg = region-ID
-    region-ID = ID of region atoms must be in to contribute to spatial averaging
-  norm arg = all or sample
-  units arg = box or lattice or reduced
-  ave args = one or running or window M
-    one = output new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  file arg = filename
-    filename = file to write results to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/spatial/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values"
-fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile 
-
    -

    Description: -

    -

    Use one or more per-atom vectors as inputs every few timesteps, bin -their values spatially into spherical shells based on current atom -coordinates, and average the bin values over longer timescales. The -resulting bin averages can be used by other output -commands such as thermo_style -custom, and can also be written to a file. -

    -

    The group specified with the command means only atoms within the group -contribute to bin averages. If the region keyword is used, the atom -must be in both the group and the specified geometric -region in order to contribute to bin averages. -

    -

    Each listed value can be an atom attribute (position, velocity, force -component), a mass or number density, or the result of a -compute or fix or the evaluation of an -atom-style variable. In the latter cases, the -compute, fix, or variable must produce a per-atom quantity, not a -global quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the fix -ave/time command. -

    -

    Computes that produce per-atom quantities are those -which have the word atom in their style name. See the doc pages for -individual fixes to determine which ones produce per-atom -quantities. Variables of style atom are the only -ones that can be used with this fix since all other styles of variable -produce global quantities. -

    -

    The per-atom values of each input vector are binned and averaged -independently of the per-atom values in other input vectors. -

    -

    Nbins specifies the number of spherical shells which will be created -between r_min and r_max centered at (origin_x, origin_y, origin_z). -

    -

    IMPORTANT NOTE: This fix works by creating an array of size Nbins by -Nvalues on each processor. Nbins is the total number of bins; Nvalues -is the number of input values specified. Each processor loops over -its atoms, tallying its values to the appropriate bin. Then the -entire array is summed across all processors. This means that using a -large number of bins will incur an overhead in memory and computational -cost (summing across processors), so be careful to use reasonable numbers -of bins. -

    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used to bin them and contribute to -the average. The final averaged quantities are generated on timesteps -that are a multiples of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. -Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. -

    -
    - -

    The origin_x, origin_y, and origin_z parameters may be specified -by either a compute or a variable. This allows, for example, the -center of the spherical bins to be attached to the center of mass of a -group of atoms. If a variable origin is used and periodic boundary -conditions are in effect, then the origin will be wrapped across -periodic boundaries whenever it changes so that it is always inside -the simulation box. -

    -
    - -

    The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. -Note that other atom attributes (including atom postitions x,y,z) can -be used as inputs to this fix by using the compute -property/atom command and then specifying -an input value from that compute. -

    -

    The density/number value means the number density is computed in -each bin, i.e. a weighting of 1 for each atom. The density/mass -value means the mass density is computed in each bin, i.e. each atom -is weighted by its mass. The resulting density is normalized by the -volume of the bin so that units of number/volume or density are -output. See the units command doc page for the -definition of density for each choice of units, e.g. gram/cm^3. -The bin volume will always be calculated in box units, independent -of the use of the units keyword in this command. -

    -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and add them to LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with -Nevery, else an error results. Users can also write code for their -own fix styles and add them to LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables of style -atom can reference thermodynamic keywords and various per-atom -attributes, or invoke other computes, fixes, or variables when they -are evaluated, so this is a very general means of generating per-atom -quantities to spatially average. -

    -
    - -

    Additional optional keywords also affect the operation of this fix. -The region keyword was discussed above. -

    -

    The norm keyword affects how averaging is done for the output -produced every Nfreq timesteps. For an all setting, a bin -quantity is summed over all atoms in all Nrepeat samples, as is the -count of atoms in the bin. The printed value for the bin is -Total-quantity / Total-count. In other words it is an average over -the entire Nfreq timescale. -

    -

    For a sample setting, the bin quantity is summed over atoms for only -a single sample, as is the count, and a "average sample value" is -computed, i.e. Sample-quantity / Sample-count. The printed value for -the bin is the average of the Nrepeat "average sample values", In -other words it is an average of an average. -

    -

    The ave keyword determines how the bin values produced every Nfreq -steps are averaged with bin values produced on previous steps that -were multiples of Nfreq, before they are accessed by another output -command or written to a file. -

    -

    If the ave setting is one, then the bin values produced on -timesteps that are multiples of Nfreq are independent of each other; -they are output as-is without further averaging. -

    -

    If the ave setting is running, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cumulative sense before being output. Each output bin value is thus -the average of the bin value produced on that timestep with all -preceding values for the same bin. This running average begins when -the fix is defined; it can only be restarted by deleting the fix via -the unfix command, or re-defining the fix by -re-specifying it. -

    -

    If the ave setting is window, then the bin values produced on -timesteps that are multiples of Nfreq are summed and averaged within -a moving "window" of time, so that the last M values for the same bin -are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then -the output on step 10000 will be the average of the individual bin -values on steps 8000,9000,10000. Outputs on early steps will average -over less than M values if they are not available. -

    -

    The units keyword determines the meaning of the distance units used -for the sphere origin and the two radial lengths. For orthogonal -simulation boxes, any of the 3 options may be used. For -non-orthogonal (triclinic) simulation boxes, only the reduced option -may be used. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacing. -

    -

    IMPORTANT NOTE: The lattice style may only be used if the lattice -spacing is the same in each direction. -

    -

    A reduced value means normalized unitless values between 0 and 1, -which represent the lower and upper faces of the simulation box -respectively. Thus an origin value of 0.5 means the center of the -box in any dimension. -

    -

    The file keyword allows a filename to be specified. Every Nfreq -timesteps, a section of bin info will be written to a text file in the -following format. A line with the timestep and number of bin is -written. Then one line per bin is written, containing the bin ID -(1-N), the coordinate of the center of the bin, the number of atoms in -the bin, and one or more calculated values. The number of values in -each line corresponds to the number of values specified in the fix -ave/spatial command. The number of atoms and the value(s) are average -quantities. If the value of the units keyword is box or -lattice, the "coord" is printed in box units. If the value of the -units keyword is reduced, the "coord" is printed in reduced units -(0-1). -

    -

    The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting. -

    -

    The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the file keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. -

    -

    By default, these header lines are as follows: -

    -
    # Spatial-averaged data for fix ID and group name
-# Timestep Number-of-bins
-# Bin r Count value1 value2 ... 
-
    -

    In the first line, ID and name are replaced with the fix-ID and group -name. The second line describes the two values that are printed at -the first of each section of output. In the third line the values are -replaced with the appropriate fields from the fix ave/spatial command. -The Coord2 and Coord3 entries in the third line only appear for 2d and -3d bins respectively. For 1d bins, the word Coord1 is replaced by -just Coord. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global array of values which can be accessed by -various output commands. The values can -only be accessed on timesteps that are multiples of Nfreq since that -is when averaging is performed. The global array has # of rows = -Nbins and # of columns = 2+Nvalues. The first column contains the -radius at the center of the shell. For units reduced, this is in -reduced units, while for units box and lattice this is in box -units. The next column has the count of atoms in that bin, and the -remaining columns are the Nvalue quantities. When the array is -accessed with an I that exceeds the current number of bins, than a 0.0 -is returned by the fix instead of an error. The array values -calculated by this fix are "intensive", since they are already -normalized by the count of atoms in each bin. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    When the ave keyword is set to running or window then the number -of bins must remain the same during the simulation, so that the -appropriate averaging can be done. This will be the case if the -simulation box size doesn't change or if the units keyword is set to -reduced. -

    -

    This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the Making of -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute, fix ave/atom, fix -ave/histo, fix ave/time, -variable, fix ave/correlate, -fix ave/spatial, -

    -

    Default: -

    -

    The option defaults are norm = all, ave = one, units = lattice, no -file output, and title 1,2,3 = strings as described above. -

    - diff --git a/doc/doc2/fix_ave_time.html b/doc/doc2/fix_ave_time.html deleted file mode 100644 index 4f2af2095d..0000000000 --- a/doc/doc2/fix_ave_time.html +++ /dev/null @@ -1,341 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ave/time command -

    -

    Syntax: -

    -
    fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ave/time = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of times to use input values for calculating averages - -
    • Nfreq = calculate averages every this many timesteps - -
    • one or more input values can be listed - -
    • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name - -
        c_ID = global scalar, vector, or array calculated by a compute with ID
-  c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
-  f_ID = global scalar, vector, or array calculated by a fix with ID
-  f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
-  v_name = global value calculated by an equal-style variable with name 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = mode or file or ave or start or off or overwrite or title1 or title2 or title3 - -
        mode arg = scalar or vector
-    scalar = all input values are global scalars
-    vector = all input values are global vectors or global arrays
-  ave args = one or running or window M
-    one = output a new average value every Nfreq steps
-    running = output cummulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  start args = Nstart
-    Nstart = start averaging on this timestep
-  off arg = M = do not average this value
-    M = value # from 1 to Nvalues
-  file arg = filename
-    filename = name of file to output time averages to
-  overwrite arg = none = overwrite output file with only latest output
-  format arg = string
-    string = C-style format string
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file, only for vector mode 
-
      - -
    -

    Examples: -

    -
    fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
-fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
-                              title1 "My output values"
-fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1 
-
    -

    Description: -

    -

    Use one or more global values as inputs every few timesteps, and -average them over longer timescales. The resulting averages can be -used by other output commands such as -thermo_style custom, and can also be written to a -file. Note that if no time averaging is done, this command can be -used as a convenient way to simply output one or more global values to -a file. -

    -

    The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. -

    -

    Each listed value can be the result of a compute or -fix or the evaluation of an equal-style -variable. In each case, the compute, fix, or variable -must produce a global quantity, not a per-atom or local quantity. If -you wish to spatial- or time-average or histogram per-atom quantities -from a compute, fix, or variable, then see the fix -ave/spatial, fix ave/atom, -or fix ave/histo commands. If you wish to sum a -per-atom quantity into a single global quantity, see the compute -reduce command. -

    -

    Computes that produce global quantities are those which -do not have the word atom in their style name. Only a few -fixes produce global quantities. See the doc pages for -individual fixes for info on which ones produce such values. -Variables of style equal are the only ones that can -be used with this fix. Variables of style atom cannot be used, -since they produce per-atom values. -

    -

    The input values must either be all scalars or all vectors (or -arrays), depending on the setting of the mode keyword. In both -cases, the averaging is performed independently on each input value. -I.e. each input scalar is averaged independently and each element of -each input vector (or array) is averaged independently. -

    -

    If mode = vector, then the input values may either be vectors or -arrays and all must be the same "length", which is the length of the -vector or number of rows in the array. If a global array is listed, -then it is the same as if the individual columns of the array had been -listed one by one. E.g. these 2 fix ave/time commands are equivalent, -since the compute rdf command creates, in this -case, a global array with 3 columns, each of length 50: -

    -
    compute myRDF all rdf 50 1 2
-fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector
-fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector 
-
    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used in order to contribute to the -average. The final averaged quantities are generated on timesteps -that are a mlutiple of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. -

    -
    - -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If mode = scalar, then if -no bracketed term is appended, the global scalar calculated by the -compute is used. If a bracketed term is appended, the Ith element of -the global vector calculated by the compute is used. If mode = -vector, then if no bracketed term is appended, the global vector -calculated by the compute is used. Or if the compute calculates an -array, all of the columns of the global array are used as if they had -been specified as individual vectors (see description above). If a -bracketed term is appended, the Ith column of the global array -calculated by the compute is used. -

    -

    Note that there is a compute reduce command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix ave/time. Or it can be a compute defined -not in your input script, but by thermodynamic -output or other fixes such as fix -nvt or fix temp/rescale. See -the doc pages for these commands which give the IDs of these computes. -Users can also write code for their own compute styles and add them -to LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If mode = scalar, then if -no bracketed term is appended, the global scalar calculated by the fix -is used. If a bracketed term is appended, the Ith element of the -global vector calculated by the fix is used. If mode = vector, then -if no bracketed term is appended, the global vector calculated by the -fix is used. Or if the fix calculates an array, all of the columns of -the global array are used as if they had been specified as individual -vectors (see description above). If a bracketed term is appended, the -Ith column of the global array calculated by the fix is used. -

    -

    Note that some fixes only produce their values on certain timesteps, -which must be compatible with Nevery, else an error will result. -Users can also write code for their own fix styles and add them to -LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Variables can only be -used as input for mode = scalar. Only equal-style variables can be -referenced. See the variable command for details. -Note that variables of style equal define a formula which can -reference individual atom properties or thermodynamic keywords, or -they can invoke other computes, fixes, or variables when they are -evaluated, so this is a very general means of specifying quantities to -time average. -

    -
    - -

    Additional optional keywords also affect the operation of this fix. -

    -

    If the mode keyword is set to scalar, then all input values must -be global scalars, or elements of global vectors. If the mode -keyword is set to vector, then all input values must be global -vectors, or columns of global arrays. They can also be global arrays, -which are converted into a series of global vectors (one per column), -as explained above. -

    -

    The ave keyword determines how the values produced every Nfreq -steps are averaged with values produced on previous steps that were -multiples of Nfreq, before they are accessed by another output -command or written to a file. -

    -

    If the ave setting is one, then the values produced on timesteps -that are multiples of Nfreq are independent of each other; they are -output as-is without further averaging. -

    -

    If the ave setting is running, then the values produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cummulative sense before being output. Each output value is thus the -average of the value produced on that timestep with all preceding -values. This running average begins when the fix is defined; it can -only be restarted by deleting the fix via the unfix -command, or by re-defining the fix by re-specifying it. -

    -

    If the ave setting is window, then the values produced on -timesteps that are multiples of Nfreq are summed and averaged within -a moving "window" of time, so that the last M values are used to -produce the output. E.g. if M = 3 and Nfreq = 1000, then the output -on step 10000 will be the average of the individual values on steps -8000,9000,10000. Outputs on early steps will average over less than M -values if they are not available. -

    -

    The start keyword specifies what timestep averaging will begin on. -The default is step 0. Often input values can be 0.0 at time 0, so -setting start to a larger value can avoid including a 0.0 in a -running or windowed average. -

    -

    The off keyword can be used to flag any of the input values. If a -value is flagged, it will not be time averaged. Instead the most -recent input value will always be stored and output. This is useful -if one of more of the inputs produced by a compute or fix or variable -are effectively constant or are simply current values. E.g. they are -being written to a file with other time-averaged values for purposes -of creating well-formatted output. -

    -

    The file keyword allows a filename to be specified. Every Nfreq -steps, one quantity or vector of quantities is written to the file for -each input value specified in the fix ave/time command. For mode = -scalar, this means a single line is written each time output is -performed. Thus the file ends up to be a series of lines, i.e. one -column of numbers for each input value. For mode = vector, an array -of numbers is written each time output is performed. The number of -rows is the length of the input vectors, and the number of columns is -the number of values. Thus the file ends up to be a series of these -array sections. -

    -

    The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting. -

    -

    The format keyword sets the numeric format of each value when it is -printed to a file via the file keyword. Note that all values are -floating point quantities. The default format is %g. You can specify -a higher precision if desired, e.g. %20.16g. -

    -

    The title1 and title2 and title3 keywords allow specification of -the strings that will be printed as the first 2 or 3 lines of the -output file, assuming the file keyword was used. LAMMPS uses -default values for each of these, so they do not need to be specified. -

    -

    By default, these header lines are as follows for mode = scalar: -

    -
    # Time-averaged data for fix ID
-# TimeStep value1 value2 ... 
-
    -

    In the first line, ID is replaced with the fix-ID. In the second line -the values are replaced with the appropriate fields from the fix -ave/time command. There is no third line in the header of the file, -so the title3 setting is ignored when mode = scalar. -

    -

    By default, these header lines are as follows for mode = vector: -

    -
    # Time-averaged data for fix ID
-# TimeStep Number-of-rows
-# Row value1 value2 ... 
-
    -

    In the first line, ID is replaced with the fix-ID. The second line -describes the two values that are printed at the first of each section -of output. In the third line the values are replaced with the -appropriate fields from the fix ave/time command. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix produces a global scalar or global vector or global array -which can be accessed by various output -commands. The values can only be -accessed on timesteps that are multiples of Nfreq since that is when -averaging is performed. -

    -

    A scalar is produced if only a single input value is averaged and -mode = scalar. A vector is produced if multiple input values are -averaged for mode = scalar, or a single input value for mode = -vector. In the first case, the length of the vector is the number of -inputs. In the second case, the length of the vector is the same as -the length of the input vector. An array is produced if multiple -input values are averaged and mode = vector. The global array has # -of rows = length of the input vectors and # of columns = number of -inputs. -

    -

    If the fix prouduces a scalar or vector, then the scalar and each -element of the vector can be either "intensive" or "extensive", -depending on whether the values contributing to the scalar or vector -element are "intensive" or "extensive". If the fix produces an array, -then all elements in the array must be the same, either "intensive" or -"extensive". If a compute or fix provides the value being time -averaged, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for -further info. Values produced by a variable are treated as intensive. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute, fix ave/atom, fix -ave/spatial, fix ave/histo, -variable, fix ave/correlate, -

    -

    Default: -

    -

    The option defaults are mode = scalar, ave = one, start = 0, no file -output, format = %g, title 1,2,3 = strings as described above, and no -off settings for any input values. -

    - diff --git a/doc/doc2/fix_aveforce.html b/doc/doc2/fix_aveforce.html deleted file mode 100644 index d7c1011cec..0000000000 --- a/doc/doc2/fix_aveforce.html +++ /dev/null @@ -1,128 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix aveforce command -

    -

    fix aveforce/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID aveforce fx fy fz keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • aveforce = style name of this fix command - -
    • fx,fy,fz = force component values (force units) - -
        any of fx,fy,fz can be a variable (see below) 
-
      -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = region - -
        region value = region-ID
-    region-ID = ID of region atoms must be in to have added force 
-
      - -
    -

    Examples: -

    -
    fix pressdown topwall aveforce 0.0 -1.0 0.0
-fix 2 bottomwall aveforce NULL -1.0 0.0 region top
-fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top 
-
    -

    Description: -

    -

    Apply an additional external force to a group of atoms in such a way -that every atom experiences the same force. This is useful for -pushing on wall or boundary atoms so that the structure of the wall -does not change over time. -

    -

    The existing force is averaged for the group of atoms, component by -component. The actual force on each atom is then set to the average -value plus the component specified in this command. This means each -atom in the group receives the same force. -

    -

    Any of the fx,fy,fz values can be specified as NULL which means the -force in that dimension is not changed. Note that this is not the -same as specifying a 0.0 value, since that sets all forces to the same -average value without adding in any additional force. -

    -

    Any of the 3 quantities defining the force components can be specified -as an equal-style variable, namely fx, fy, fz. -If the value is a variable, it should be specified as v_name, where -name is the variable name. In this case, the variable will be -evaluated each timestep, and its value used to determine the average -force. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent average force. -

    -

    If the region keyword is used, the atom must also be in the -specified geometric region in order to have force added -to it. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global 3-vector of forces, which can be accessed -by various output commands. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix setforce, fix addforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_balance.html b/doc/doc2/fix_balance.html deleted file mode 100644 index 5634916d21..0000000000 --- a/doc/doc2/fix_balance.html +++ /dev/null @@ -1,361 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix balance command -

    -

    Syntax: -

    -
    fix ID group-ID balance Nfreq thresh style args keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • balance = style name of this fix command - -
    • Nfreq = perform dynamic load balancing every this many steps - -
    • thresh = imbalance threshhold that must be exceeded to perform a re-balance - -
    • style = shift or rcb - -
        shift args = dimstr Niter stopthresh
-    dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
-    Niter = # of times to iterate within each dimension of dimstr sequence
-    stopthresh = stop balancing when this imbalance threshhold is reached
-  rcb args = none 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = out - -
        out value = filename
-    filename = write each processor's sub-domain to a file, at each re-balancing 
-
      - -
    -

    Examples: -

    -
    fix 2 all balance 1000 1.05 shift x 10 1.05
-fix 2 all balance 100 0.9 shift xy 20 1.1 out tmp.balance
-fix 2 all balance 1000 1.1 rcb 
-
    -

    Description: -

    -

    This command adjusts the size and shape of processor sub-domains -within the simulation box, to attempt to balance the number of -particles and thus the computational cost (load) evenly across -processors. The load balancing is "dynamic" in the sense that -rebalancing is performed periodically during the simulation. To -perform "static" balancing, before or between runs, see the -balance command. -

    -

    Load-balancing is typically only useful if the particles in the -simulation box have a spatially-varying density distribution. E.g. a -model of a vapor/liquid interface, or a solid with an irregular-shaped -geometry containing void regions. In this case, the LAMMPS default of -dividing the simulation box volume into a regular-spaced grid of 3d -bricks, with one equal-volume sub-domain per processor, may assign -very different numbers of particles per processor. This can lead to -poor performance when the simulation is run in parallel. -

    -

    Note that the processors command allows some control -over how the box volume is split across processors. Specifically, for -a Px by Py by Pz grid of processors, it allows choice of Px, Py, and -Pz, subject to the constraint that Px * Py * Pz = P, the total number -of processors. This is sufficient to achieve good load-balance for -some problems on some processor counts. However, all the processor -sub-domains will still have the same shape and same volume. -

    -

    On a particular timestep, a load-balancing operation is only performed -if the current "imbalance factor" in particles owned by each processor -exceeds the specified thresh parameter. The imbalance factor is -defined as the maximum number of particles owned by any processor, -divided by the average number of particles per processor. Thus an -imbalance factor of 1.0 is perfect balance. -

    -

    As an example, for 10000 particles running on 10 processors, if the -most heavily loaded processor has 1200 particles, then the factor is -1.2, meaning there is a 20% imbalance. Note that re-balances can be -forced even if the current balance is perfect (1.0) be specifying a -thresh < 1.0. -

    -

    IMPORTANT NOTE: This command attempts to minimize the imbalance -factor, as defined above. But depending on the method a perfect -balance (1.0) may not be achieved. For example, "grid" methods -(defined below) that create a logical 3d grid cannot achieve perfect -balance for many irregular distributions of particles. Likewise, if a -portion of the system is a perfect lattice, e.g. the initial system is -generated by the create_atoms command, then "grid" -methods may be unable to achieve exact balance. This is because -entire lattice planes will be owned or not owned by a single -processor. -

    -

    IMPORTANT NOTE: The imbalance factor is also an estimate of the -maximum speed-up you can hope to achieve by running a perfectly -balanced simulation versus an imbalanced one. In the example above, -the 10000 particle simulation could run up to 20% faster if it were -perfectly balanced, versus when imbalanced. However, computational -cost is not strictly proportional to particle count, and changing the -relative size and shape of processor sub-domains may lead to -additional computational and communication overheads, e.g. in the PPPM -solver used via the kspace_style command. Thus -you should benchmark the run times of a simulation before and after -balancing. -

    -
    - -

    The method used to perform a load balance is specified by one of the -listed styles, which are described in detail below. There are 2 kinds -of styles. -

    -

    The shift style is a "grid" method which produces a logical 3d grid -of processors. It operates by changing the cutting planes (or lines) -between processors in 3d (or 2d), to adjust the volume (area in 2d) -assigned to each processor, as in the following 2d diagram where -processor sub-domains are shown and atoms are colored by the processor -that owns them. The leftmost diagram is the default partitioning of -the simulation box across processors (one sub-box for each of 16 -processors); the middle diagram is after a "grid" method has been -applied. -

    -
    -
    -

    The rcb style is a "tiling" method which does not produce a logical -3d grid of processors. Rather it tiles the simulation domain with -rectangular sub-boxes of varying size and shape in an irregular -fashion so as to have equal numbers of particles in each sub-box, as -in the rightmost diagram above. -

    -

    The "grid" methods can be used with either of the -comm_style command options, brick or tiled. The -"tiling" methods can only be used with comm_style -tiled. -

    -

    When a "grid" method is specified, the current domain partitioning can -be either a logical 3d grid or a tiled partitioning. In the former -case, the current logical 3d grid is used as a starting point and -changes are made to improve the imbalance factor. In the latter case, -the tiled partitioning is discarded and a logical 3d grid is created -with uniform spacing in all dimensions. This is the starting point -for the balancing operation. -

    -

    When a "tiling" method is specified, the current domain partitioning -("grid" or "tiled") is ignored, and a new partitioning is computed -from scratch. -

    -
    - -

    The group-ID is currently ignored. In the future it may be used to -determine what particles are considered for balancing. Normally it -would only makes sense to use the all group. But in some cases it -may be useful to balance on a subset of the particles, e.g. when -modeling large nanoparticles in a background of small solvent -particles. -

    -

    The Nfreq setting determines how often a rebalance is performed. If -Nfreq > 0, then rebalancing will occur every Nfreq steps. Each -time a rebalance occurs, a reneighboring is triggered, so Nfreq -should not be too small. If Nfreq = 0, then rebalancing will be -done every time reneighboring normally occurs, as determined by the -the neighbor and neigh_modify -command settings. -

    -

    On rebalance steps, rebalancing will only be attempted if the current -imbalance factor, as defined above, exceeds the thresh setting. -

    -
    - -

    The shift style invokes a "grid" method for balancing, as described -above. It changes the positions of cutting planes between processors -in an iterative fashion, seeking to reduce the imbalance factor. -

    -

    The dimstr argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, -since there is no advantage to balancing on a dimension more than -once. You should normally only list dimensions where you expect there -to be a density variation in the particles. -

    -

    Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in dimstr, one dimension at a time. For a single -dimension, the balancing operation (described below) is iterated on up -to Niter times. After each dimension finishes, the imbalance factor -is re-computed, and the balancing operation halts if the stopthresh -criterion is met. -

    -

    A rebalance operation in a single dimension is performed using a -density-dependent recursive multisectioning algorithm, where the -position of each cutting plane (line in 2d) in the dimension is -adjusted independently. This is similar to a recursive bisectioning -for a single value, except that the bounds used for each bisectioning -take advantage of information from neighboring cuts if possible, as -well as counts of particles at the bounds on either side of each cuts, -which themselves were cuts in previous iterations. The latter is used -to infer a density of pariticles near each of the current cuts. At -each iteration, the count of particles on either side of each plane is -tallied. If the counts do not match the target value for the plane, -the position of the cut is adjusted based on the local density. The -low and high bounds are adjusted on each iteration, using new count -information, so that they become closer together over time. Thus as -the recursion progresses, the count of particles on either side of the -plane gets closer to the target value. -

    -

    The density-dependent part of this algorithm is often an advantage -when you rebalance a system that is already nearly balanced. It -typically converges more quickly than the geometric bisectioning -algorithm used by the balance command. However, if can -be a disadvantage if you attempt to rebalance a system that is far -from balanced, and converge more slowly. In this case you probably -want to use the balance command before starting a run, -so that you begin the run with a balanced system. -

    -

    Once the rebalancing is complete and final processor sub-domains -assigned, particles migrate to their new owning processor as part of -the normal reneighboring procedure. -

    -

    IMPORTANT NOTE: At each rebalance operation, the bisectioning for each -cutting plane (line in 2d) typcially starts with low and high bounds -separated by the extent of a processor's sub-domain in one dimension. -The size of this bracketing region shrinks based on the local density, -as described above, which should typically be 1/2 or more every -iteration. Thus if Niter is specified as 10, the cutting plane will -typically be positioned to better than 1 part in 1000 accuracy -(relative to the perfect target position). For Niter = 20, it will -be accurate to better than 1 part in a million. Thus there is no need -to set Niter to a large value. This is especially true if you are -rebalancing often enough that each time you expect only an incremental -adjustement in the cutting planes is necessary. LAMMPS will check if -the threshold accuracy is reached (in a dimension) is less iterations -than Niter and exit early. -

    -
    - -

    The rcb style invokes a "tiled" method for balancing, as described -above. It performs a recursive coordinate bisectioning (RCB) of the -simulation domain. The basic idea is as follows. -

    -

    The simulation domain is cut into 2 boxes by an axis-aligned cut in -the longest dimension, leaving one new box on either side of the cut. -All the processors are also partitioned into 2 groups, half assigned -to the box on the lower side of the cut, and half to the box on the -upper side. (If the processor count is odd, one side gets an extra -processor.) The cut is positioned so that the number of atoms in the -lower box is exactly the number that the processors assigned to that -box should own for load balance to be perfect. This also makes load -balance for the upper box perfect. The positioning is done -iteratively, by a bisectioning method. Note that counting atoms on -either side of the cut requires communication between all processors -at each iteration. -

    -

    That is the procedure for the first cut. Subsequent cuts are made -recursively, in exactly the same manner. The subset of processors -assigned to each box make a new cut in the longest dimension of that -box, splitting the box, the subset of processsors, and the atoms in -the box in two. The recursion continues until every processor is -assigned a sub-box of the entire simulation domain, and owns the atoms -in that sub-box. -

    -
    - -

    The out keyword writes a text file to the specified filename with -the results of each rebalancing operation. The file contains the -bounds of the sub-domain for each processor after the balancing -operation completes. The format of the file is compatible with the -Pizza.py mdump tool which has support for manipulating and -visualizing mesh files. An example is shown here for a balancing by 4 -processors for a 2d problem: -

    -
    ITEM: TIMESTEP
-0
-ITEM: NUMBER OF NODES
-16
-ITEM: BOX BOUNDS
-0 10
-0 10
-0 10
-ITEM: NODES
-1 1 0 0 0
-2 1 5 0 0
-3 1 5 5 0
-4 1 0 5 0
-5 1 5 0 0
-6 1 10 0 0
-7 1 10 5 0
-8 1 5 5 0
-9 1 0 5 0
-10 1 5 5 0
-11 1 5 10 0
-12 1 10 5 0
-13 1 5 5 0
-14 1 10 5 0
-15 1 10 10 0
-16 1 5 10 0
-ITEM: TIMESTEP
-0
-ITEM: NUMBER OF SQUARES
-4
-ITEM: SQUARES
-1 1 1 2 3 4
-2 1 5 6 7 8
-3 1 9 10 11 12
-4 1 13 14 15 16 
-
    -

    The coordinates of all the vertices are listed in the NODES section, 5 -per processor. Note that the 4 sub-domains share vertices, so there -will be duplicate nodes in the list. -

    -

    The "SQUARES" section lists the node IDs of the 4 vertices in a -rectangle for each processor (1 to 4). -

    -

    For a 3d problem, the syntax is similar with 8 vertices listed for -each processor, instead of 4, and "SQUARES" replaced by "CUBES". -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar which is the imbalance factor -after the most recent rebalance and a global vector of length 3 with -additional information about the most recent rebalancing. The 3 -values in the vector are as follows: -

    -
    • 1 = max # of particles per processor -
    • 2 = total # iterations performed in last rebalance -
    • 3 = imbalance factor right before the last rebalance was performed -
    -

    As explained above, the imbalance factor is the ratio of the maximum -number of particles on any processor to the average number of -particles per processor. -

    -

    These quantities can be accessed by various output -commands. The scalar and vector values -calculated by this fix are "intensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -
    - -

    Restrictions: -

    -

    For 2d simulations, a "z" cannot appear in dimstr for the shift -style. -

    -

    Related commands: -

    -

    processors, balance -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_bond_break.html b/doc/doc2/fix_bond_break.html deleted file mode 100644 index 2bb8d5e667..0000000000 --- a/doc/doc2/fix_bond_break.html +++ /dev/null @@ -1,158 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix bond/break command -

    -

    Syntax: -

    -
    fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • bond/break = style name of this fix command - -
    • Nevery = attempt bond breaking every this many steps - -
    • bondtype = type of bonds to break - -
    • Rmax = bond longer than Rmax can break (distance units) - -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = prob - -
        prob values = fraction seed
-    fraction = break a bond with this probability if otherwise eligible
-    seed = random number seed (positive integer) 
-
      - -
    -

    Examples: -

    -
    fix 5 all bond/break 10 2 1.2
-fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829 
-
    -

    Description: -

    -

    Break bonds between pairs of atoms as a simulation runs according to -specified criteria. This can be used to model the dissolution of a -polymer network due to stretching of the simulation box or other -deformations. In this context, a bond means an interaction between a -pair of atoms computed by the bond_style command. -Once the bond is broken it will be permanently deleted, as will all -angle, dihedral, and improper interactions that bond is part of. -

    -

    This is different than a pairwise bond-order -potential such as Tersoff or AIREBO which infers bonds and many-body -interactions based on the current geometry of a small cluster of atoms -and effectively creates and destroys bonds and higher-order many-body -interactions from timestep to timestep as atoms move. -

    -

    A check for possible bond breakage is performed every Nevery -timesteps. If two bonded atoms I,J are further than a distance Rmax -of each other, if the bond is of type bondtype, and if both I and J -are in the specified fix group, then I,J is labeled as a "possible" -bond to break. -

    -

    If several bonds involving an atom are stretched, it may have multiple -possible bonds to break. Every atom checks its list of possible bonds -to break and labels the longest such bond as its "sole" bond to break. -After this is done, if atom I is bonded to atom J in its sole bond, -and atom J is bonded to atom I in its sole bond, then the I,J bond is -"eligible" to be broken. -

    -

    Note that these rules mean an atom will only be part of at most one -broken bond on a given timestep. It also means that if atom I chooses -atom J as its sole partner, but atom J chooses atom K is its sole -partner (due to Rjk > Rij), then this means atom I will not be part of -a broken bond on this timestep, even if it has other possible bond -partners. -

    -

    The prob keyword can effect whether an eligible bond is actually -broken. The fraction setting must be a value between 0.0 and 1.0. -A uniform random number between 0.0 and 1.0 is generated and the -eligible bond is only broken if the random number < fraction. -

    -

    When a bond is broken, data structures within LAMMPS that store bond -topology are updated to reflect the breakage. Likewise, if the bond -is part of a 3-body (angle) or 4-body (dihedral, improper) -interaction, that interaction is removed as well. These changes -typically affect pairwise interactions between atoms that used to be -part of bonds, angles, etc. -

    -

    IMPORTANT NOTE: One data structure that is not updated when a bond -breaks are the molecule IDs stored by each atom. Even though -one molecule becomes two moleclues due to the broken bond, all atoms -in both new moleclues retain their original molecule IDs. -

    -

    Computationally, each timestep this fix operates, it loops over all -the bonds in the system and computes distances between pairs of bonded -atoms. It also communicates between neighboring processors to -coordinate which bonds are broken. Moreover, if any bonds are broken, -neighbor lists must be immediately updated on the same timestep. This -is to insure that any pairwise interactions that should be turned "on" -due to a bond breaking, because they are no longer excluded by the -presence of the bond and the settings of the -special_bonds command, will be immediately -recognized. All of these operations increase the cost of a timestep. -Thus you should be cautious about invoking this fix too frequently. -

    -

    You can dump out snapshots of the current bond topology via the dump -local command. -

    -

    IMPORTANT NOTE: Breaking a bond typically alters the energy of a -system. You should be careful not to choose bond breaking criteria -that induce a dramatic change in energy. For example, if you define a -very stiff harmonic bond and break it when 2 atoms are separated by a -distance far from the equilibribum bond length, then the 2 atoms will -be dramatically released when the bond is broken. More generally, you -may need to thermostat your system to compensate for energy changes -resulting from broken bonds (and angles, dihedrals, impropers). -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes two statistics which it stores in a global vector of -length 2, which can be accessed by various output -commands. The vector values calculated -by this fix are "intensive". -

    -

    These are the 2 quantities: -

    -
    • (1) # of bonds broken on the most recent breakage timestep -
    • (2) cummulative # of bonds broken -
    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix bond/create, fix -bond/swap, dump local, -special_bonds -

    -

    Default: -

    -

    The option defaults are prob = 1.0. -

    - diff --git a/doc/doc2/fix_bond_create.html b/doc/doc2/fix_bond_create.html deleted file mode 100644 index f0cd61dbad..0000000000 --- a/doc/doc2/fix_bond_create.html +++ /dev/null @@ -1,256 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix bond/create command -

    -

    Syntax: -

    -
    fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • bond/create = style name of this fix command - -
    • Nevery = attempt bond creation every this many steps - -
    • itype,jtype = atoms of itype can bond to atoms of jtype - -
    • Rmin = 2 atoms separated by less than Rmin can bond (distance units) - -
    • bondtype = type of created bonds - -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = iparam or jparam or prob or atype or dtype or itype - -
        iparam values = maxbond, newtype
-    maxbond = max # of bonds of bondtype the itype atom can have
-    newtype = change the itype atom to this type when maxbonds exist
-  jparam values = maxbond, newtype
-    maxbond = max # of bonds of bondtype the jtype atom can have
-    newtype = change the jtype atom to this type when maxbonds exist
-  prob values = fraction seed
-    fraction = create a bond with this probability if otherwise eligible
-    seed = random number seed (positive integer)
-  atype value = angletype
-    angletype = type of created angles
-  dtype value = dihedraltype
-    dihedraltype = type of created dihedrals
-  itype value = impropertype
-    impropertype = type of created impropers 
-
      - -
    -

    Examples: -

    -
    fix 5 all bond/create 10 1 2 0.8 1
-fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
-fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2 
-
    -

    Description: -

    -

    Create bonds between pairs of atoms as a simulation runs according to -specified criteria. This can be used to model cross-linking of -polymers, the formation of a percolation network, etc. In this -context, a bond means an interaction between a pair of atoms computed -by the bond_style command. Once the bond is created -it will be permanently in place. Optionally, the creation of a bond -can also create angle, dihedral, and improper interactions that bond -is part of. See the discussion of the atype, dtype, and itype -keywords below. -

    -

    This is different than a pairwise bond-order -potential such as Tersoff or AIREBO which infers bonds and many-body -interactions based on the current geometry of a small cluster of atoms -and effectively creates and destroys bonds and higher-order many-body -interactions from timestep to timestep as atoms move. -

    -

    A check for possible new bonds is performed every Nevery timesteps. -If two atoms I,J are within a distance Rmin of each other, if I is -of atom type itype, if J is of atom type jtype, if both I and J -are in the specified fix group, if a bond does not already exist -between I and J, and if both I and J meet their respective maxbond -requirement (explained below), then I,J is labeled as a "possible" -bond pair. -

    -

    If several atoms are close to an atom, it may have multiple possible -bond partners. Every atom checks its list of possible bond partners -and labels the closest such partner as its "sole" bond partner. After -this is done, if atom I has atom J as its sole partner, and atom J has -atom I as its sole partner, then the I,J bond is "eligible" to be -formed. -

    -

    Note that these rules mean an atom will only be part of at most one -created bond on a given timestep. It also means that if atom I -chooses atom J as its sole partner, but atom J chooses atom K is its -sole partner (due to Rjk < Rij), then this means atom I will not form -a bond on this timestep, even if it has other possible bond partners. -

    -

    It is permissible to have itype = jtype. Rmin must be <= the -pairwise cutoff distance between itype and jtype atoms, as defined -by the pair_style command. -

    -

    The iparam and jparam keywords can be used to limit the bonding -functionality of the participating atoms. Each atom keeps track of -how many bonds of bondtype it already has. If atom I of -itype already has maxbond bonds (as set by the iparam -keyword), then it will not form any more. Likewise for atom J. If -maxbond is set to 0, then there is no limit on the number of bonds -that can be formed with that atom. -

    -

    The newtype value for iparam and jparam can be used to change -the atom type of atom I or J when it reaches maxbond number of bonds -of type bondtype. This means it can now interact in a pairwise -fashion with other atoms in a different way by specifying different -pair_coeff coefficients. If you do not wish the -atom type to change, simply specify newtype as itype or jtype. -

    -

    The prob keyword can also effect whether an eligible bond is -actually created. The fraction setting must be a value between 0.0 -and 1.0. A uniform random number between 0.0 and 1.0 is generated and -the eligible bond is only created if the random number < fraction. -

    -

    Any bond that is created is assigned a bond type of bondtype -

    -

    When a bond is created, data structures within LAMMPS that store bond -topology are updated to reflect the creation. If the bond is part of -new 3-body (angle) or 4-body (dihedral, improper) interactions, you -can choose to create new angles, dihedrals, impropers as well, using -the atype, dtype, and itype keywords. All of these changes -typically affect pairwise interactions between atoms that are now part -of new bonds, angles, etc. -

    -

    IMPORTANT NOTE: One data structure that is not updated when a bond -breaks are the molecule IDs stored by each atom. Even though two -molecules become one moleclue due to the created bond, all atoms in -the new moleclue retain their original molecule IDs. -

    -

    If the atype keyword is used and if an angle potential is defined -via the angle_style command, then any new 3-body -interactions inferred by the creation of a bond will create new angles -of type angletype, with parameters assigned by the corresponding -angle_coeff command. Likewise, the dtype and -itype keywords will create new dihedrals and impropers of type -dihedraltype and impropertype. -

    -

    IMPORTANT NOTE: To create a new bond, the internal LAMMPS data -structures that store this information must have space for it. When -LAMMPS is initialized from a data file, the list of bonds is scanned -and the maximum number of bonds per atom is tallied. If some atom -will acquire more bonds than this limit as this fix operates, then the -"extra bond per atom" parameter must be set to allow for it. Ditto -for "extra angle per atom", "extra dihedral per atom", and "extra -improper per atom" if angles, dihedrals, or impropers are being added -when bonds are created. See the read_data or -create_box command for more details. Note that a -data file with no atoms can be used if you wish to add unbonded atoms -via the create atoms command, e.g. for a -percolation simulation. -

    -

    IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a -list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond -topology of the system) for use in weighting pairwise interactions for -bonded atoms. Note that adding a single bond always adds a new 1st -neighbor but may also induce *many* new 2nd and 3rd neighbors, -depending on the molecular topology of your system. The "extra -special per atom" parameter must typically be set to allow for the new -maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. -There are 3 ways to do this. See the read_data or -create_box or "special_bonds extra" commands for -details. -

    -

    IMPORTANT NOTE: Even if you do not use the atype, dtype, or -itype keywords, the list of topological neighbors is updated for -atoms affected by the new bond. This in turn affects which neighbors -are considered for pairwise interactions, using the weighting rules -set by the special_bonds command. Consider a new -bond created between atoms I,J. If J has a bonded neighbor K, then K -becomes a 2nd neighbor of I. Even if the atype keyword is not used -to create angle I-J-K, the pairwise interaction between I and K will -be potentially turned off or weighted by the 1-3 weighting specified -by the special_bonds command. This is the case -even if the "angle yes" option was used with that command. The same -is true for 3rd neighbors (1-4 interactions), the dtype keyword, and -the "dihedral yes" option used with the -special_bonds command. -

    -

    Note that even if your simulation starts with no bonds, you must -define a bond_style and use the -bond_coeff command to specify coefficients for the -bondtype. Similarly, if new atom types are specified by the -iparam or jparam keywords, they must be within the range of atom -types allowed by the simulation and pairwise coefficients must be -specified for the new types. -

    -

    Computationally, each timestep this fix operates, it loops over -neighbor lists and computes distances between pairs of atoms in the -list. It also communicates between neighboring processors to -coordinate which bonds are created. Moreover, if any bonds are -created, neighbor lists must be immediately updated on the same -timestep. This is to insure that any pairwise interactions that -should be turned "off" due to a bond creation, because they are now -excluded by the presence of the bond and the settings of the -special_bonds command, will be immediately -recognized. All of these operations increase the cost of a timestep. -Thus you should be cautious about invoking this fix too frequently. -

    -

    You can dump out snapshots of the current bond topology via the dump -local command. -

    -

    IMPORTANT NOTE: Creating a bond typically alters the energy of a -system. You should be careful not to choose bond creation criteria -that induce a dramatic change in energy. For example, if you define a -very stiff harmonic bond and create it when 2 atoms are separated by a -distance far from the equilibribum bond length, then the 2 atoms will -oscillate dramatically when the bond is formed. More generally, you -may need to thermostat your system to compensate for energy changes -resulting from created bonds (and angles, dihedrals, impropers). -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes two statistics which it stores in a global vector of -length 2, which can be accessed by various output -commands. The vector values calculated -by this fix are "intensive". -

    -

    These are the 2 quantities: -

    -
    • (1) # of bonds created on the most recent creation timestep -
    • (2) cummulative # of bonds created -
    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix bond/break, fix -bond/swap, dump local, -special_bonds -

    -

    Default: -

    -

    The option defaults are iparam = (0,itype), jparam = (0,jtype), and -prob = 1.0. -

    - diff --git a/doc/doc2/fix_bond_swap.html b/doc/doc2/fix_bond_swap.html deleted file mode 100644 index fbf2288613..0000000000 --- a/doc/doc2/fix_bond_swap.html +++ /dev/null @@ -1,199 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix bond/swap command -

    -

    Syntax: -

    -
    fix ID group-ID bond/swap Nevery fraction cutoff seed 
-
    -
    • ID, group-ID are documented in fix command -
    • bond/swap = style name of this fix command -
    • Nevery = attempt bond swapping every this many steps -
    • fraction = fraction of group atoms to consider for swapping -
    • cutoff = distance at which swapping will be considered (distance units) -
    • seed = random # seed (positive integer) -
    -

    Examples: -

    -
    fix 1 all bond/swap 50 0.5 1.3 598934 
-
    -

    Description: -

    -

    In a simulation of polymer chains, this command attempts to swap bonds -between two different chains, effectively grafting the end of one -chain onto another chain and vice versa. This is done via Monte Carlo -rules using the Boltzmann acceptance criterion. The purpose is to -equilibrate the polymer chain conformations more rapidly than dynamics -alone would do it, by enabling instantaneous large conformational -changes in a dense polymer melt. The polymer chains should thus more -rapidly converge to the proper end-to-end distances and radii of -gyration. It is designed for use with systems of -FENE or harmonic bead-spring -polymer chains where each polymer is a linear chain of monomers, but -LAMMPS does not enforce this requirement, i.e. any -bond_style can be used. -

    -

    A schematic of the kinds of bond swaps that can occur is shown here: -

    -
    -
    -

    On the left, the red and blue chains have two monomers A1 and B1 close -to each other, which are currently bonded to monomers A2 and B2 -respectively within their own chains. The bond swap operation will -attempt to delete the A1-A2 and B1-B2 bonds and replace them with -A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the -two chains on the right are the result and each polymer chain has -undergone a dramatic conformational change. This reference, -(Sides) provides more details on how the algorithm works and -its application: -

    -

    The bond swapping operation is invoked every Nevery timesteps. If -any bond is swapped, a re-build of the neighbor lists is triggered, -since a swap alters the list of which neighbors are considered for -pairwise interaction. At each invocation, each processor considers a -random specified fraction of its atoms as potential swapping -monomers for this timestep. Choosing a small fraction value can -reduce the likelihood of a reverse swap occurring soon after an -initial swap. -

    -

    For each monomer A1, its neighbors are examined to find a possible B1 -monomer. Both A1 and B1 must be in the fix group, their separation -must be less than the specified cutoff, and the molecule IDs of A1 -and B1 must be the same (see below). If a suitable partner is found, -the energy change due to swapping the 2 bonds is computed. This -includes changes in pairwise, bond, and angle energies due to the -altered connectivity of the 2 chains. Dihedral and improper -interactions are not allowed to be defined when this fix is used. -

    -

    If the energy decreases due to the swap operation, the bond swap is -accepted. If the energy increases it is accepted with probability -exp(-delta/kT) where delta is the increase in energy, k is the -Boltzmann constant, and T is the current temperature of the system. -Whether the swap is accepted or rejected, no other swaps are attempted -by this processor on this timestep. -

    -

    The criterion for matching molecule IDs is how bond swaps performed by -this fix conserve chain length. To use this features you must setup -the molecule IDs for your polymer chains in a certain way, typically -in the data file, read by the read_data comand. -Consider a system of 6-mer chains. You have 2 choices. If the -molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then -swaps will conserve chain length. For a particular momoner there will -be only one other monomer on another chain which is a potential swap -partner. If the molecule IDs for monomers on each chain are set to -1,2,3,3,2,1 then swaps will conserve chain length but swaps will be -able to occur at either end of a chain. Thus for a particular monomer -there will be 2 possible swap partners on another chain. In this -scenario, swaps can also occur within a single chain, i.e. the two -ends of a chain swap with each other. -

    -

    IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way, -where all monomers on a single chain are assigned the same ID -(different for each chain), then swaps will only occur within the same -chain. If you assign the same molecule ID to all monomers in all -chains then inter-chain swaps will occur, but they will not conserve -chain length. Neither of these scenarios is probably what you want -for this fix. -

    -

    IMPORTANT NOTE: When a bond swap occurs the image flags of monomers in -the new polymer chains can become inconsistent. See the -dump command for a discussion of image flags. This is not -an issue for running dynamics, but can affect calculation of some -diagnostic quantities or the printing of unwrapped coordinates to a -dump file. -

    -
    - -

    This fix computes a temperature each time it is invoked for use by the -Boltzmann criterion. To do this, the fix creates its own compute of -style temp, as if this command had been issued: -

    -
    compute fix-ID_temp all temp 
-
    -

    See the compute temp command for details. Note -that the ID of the new compute is the fix-ID with underscore + "temp" -appended and the group for the new compute is "all", so that the -temperature of the entire system is used. -

    -

    Note that this is NOT the compute used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -compute_modify command or print this temperature -during thermodyanmic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp will have no -effect on this fix. -

    -
    - -

    Restart, fix_modify, thermo output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. Also note that -each processor generates possible swaps independently of other -processors. Thus if you repeat the same simulation on a different number -of processors, the specific swaps performed will be different. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a compute you have -defined to this fix which will be used to compute the temperature for -the Boltzmann criterion. -

    -

    This fix computes two statistical quantities as a global 2-vector of -output, which can be accessed by various output -commands. The first component of the -vector is the cummulative number of swaps performed by all processors. -The second component of the vector is the cummulative number of swaps -attempted (whether accepted or rejected). Note that a swap "attempt" -only occurs when swap partners meeting the criteria described above -are found on a particular timestep. The vector values calculated by -this fix are "intensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    The setings of the "special_bond" command must be 0,1,1 in order to -use this fix, which is typical of bead-spring chains with FENE or -harmonic bonds. This means that pairwise interactions between bonded -atoms are turned off, but are turned on between atoms two or three -hops away along the chain backbone. -

    -

    Currently, energy changes in dihedral and improper interactions due to -a bond swap are not considered. Thus a simulation that uses this fix -cannot use a dihedral or improper potential. -

    -

    Related commands: -

    -

    fix atom/swap -

    -

    Default: none -

    -
    - - - -

    (Sides) Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, -199-208 (2004). -

    - diff --git a/doc/doc2/fix_box_relax.html b/doc/doc2/fix_box_relax.html deleted file mode 100644 index 13af69fe32..0000000000 --- a/doc/doc2/fix_box_relax.html +++ /dev/null @@ -1,369 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix box/relax command -

    -

    Syntax: -

    -
    fix ID group-ID box/relax keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • box/relax = style name of this fix command - -
      one or more keyword value pairs may be appended
-keyword = iso or aniso or tri or x or y or z or xy or yz or xz or couple or nreset or vmax or dilate or scaleyz or scalexz or scalexy or fixedpoint 
-  iso or aniso or tri value = Ptarget = desired pressure (pressure units)
-  x or y or z or xy or yz or xz value = Ptarget = desired pressure (pressure units)
-  couple = none or xyz or xy or yz or xz
-  nreset value = reset reference cell every this many minimizer iterations
-  vmax value = fraction = max allowed volume change in one iteration
-  dilate value = all or partial 
-  scaleyz value = yes or no = scale yz with lz
-  scalexz value = yes or no = scale xz with lz
-  scalexy value = yes or no = scale xy with ly
-  fixedpoint values = x y z
-    x,y,z = perform relaxation dilation/contraction around this point (distance units) 
-
      - -
    -

    Examples: -

    -
    fix 1 all box/relax iso 0.0 vmax 0.001
-fix 2 water box/relax aniso 0.0 dilate partial
-fix 2 ice box/relax tri 0.0 couple xy nreset 100 
-
    -

    Description: -

    -

    Apply an external pressure or stress tensor to the simulation box -during an energy minimization. This allows the box -size and shape to vary during the iterations of the minimizer so that -the final configuration will be both an energy minimum for the -potential energy of the atoms, and the system pressure tensor will be -close to the specified external tensor. Conceptually, specifying a -positive pressure is like squeezing on the simulation box; a negative -pressure typically allows the box to expand. -

    -
    - -

    The external pressure tensor is specified using one or more of the -iso, aniso, tri, x, y, z, xy, xz, yz, and couple -keywords. These keywords give you the ability to specify all 6 -components of an external stress tensor, and to couple various of -these components together so that the dimensions they represent are -varied together during the mimimization. -

    -

    Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). -Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The create_box, read -data, and read_restart commands -specify whether the simulation box is orthogonal or non-orthogonal -(triclinic) and explain the meaning of the xy,xz,yz tilt factors. -

    -

    The target pressures Ptarget for each of the 6 components of the -stress tensor can be specified independently via the x, y, z, -xy, xz, yz keywords, which correspond to the 6 simulation box -dimensions. For example, if the y keyword is used, the y-box length -will change during the minimization. If the xy keyword is used, the -xy tilt factor will change. A box dimension will not change if that -component is not specified. -

    -

    Note that in order to use the xy, xz, or yz keywords, the -simulation box must be triclinic, even if its initial tilt factors are -0.0. -

    -

    When the size of the simulation box changes, all atoms are re-scaled -to new positions, unless the keyword dilate is specified with a -value of partial, in which case only the atoms in the fix group are -re-scaled. This can be useful for leaving the coordinates of atoms in -a solid substrate unchanged and controlling the pressure of a -surrounding fluid. -

    -

    The scaleyz, scalexz, and scalexy keywords control whether or -not the corresponding tilt factors are scaled with the associated box -dimensions when relaxing triclinic periodic cells. The default -values yes will turn on scaling, which corresponds to adjusting the -linear dimensions of the cell while preserving its shape. Choosing -no ensures that the tilt factors are not scaled with the box -dimensions. See below for restrictions and default values in different -situations. In older versions of LAMMPS, scaling of tilt factors was -not performed. The old behavior can be recovered by setting all three -scale keywords to no. -

    -

    The fixedpoint keyword specifies the fixed point for cell relaxation. -By default, it is the center of the box. Whatever point is -chosen will not move during the simulation. For example, if the lower -periodic boundaries pass through (0,0,0), and this point is provided -to fixedpoint, then the lower periodic boundaries will remain at -(0,0,0), while the upper periodic boundaries will move twice as -far. In all cases, the particle positions at each iteration are -unaffected by the chosen value, except that all particles are -displaced by the same amount, different on each iteration. -

    -

    IMPORTANT NOTE: Appling an external pressure to tilt dimensions xy, -xz, yz can sometimes result in arbitrarily large values of the -tilt factors, i.e. a dramatically deformed simulation box. This -typically indicates that there is something badly wrong with how the -simulation was constructed. The two most common sources of this error -are applying a shear stress to a liquid system or specifying an -external shear stress tensor that exceeds the yield stress of the -solid. In either case the minimization may converge to a bogus -conformation or not converge at all. Also note that if the box shape -tilts to an extreme shape, LAMMPS will run less efficiently, due to -the large volume of communication needed to acquire ghost atoms around -a processor's irregular-shaped sub-domain. For extreme values of -tilt, LAMMPS may also lose atoms and generate an error. -

    -

    IMPORTANT NOTE: Performing a minimization with this fix is not a -mathematically well-defined minimization problem. This is because the -objective function being minimized changes if the box size/shape -changes. In practice this means the minimizer can get "stuck" before -you have reached the desired tolerance. The solution to this is to -restart the minmizer from the new adjusted box size/shape, since that -creates a new objective function valid for the new box size/shape. -Repeat as necessary until the box size/shape has reached its new -equilibrium. -

    -
    - -
    - -
    - -

    The couple keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, xz -means the Pxx and Pzz components of the stress tensor are coupled. -Xyz means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -Ptarget values for any coupled dimensions must be identical. -Couple xyz can be used for a 2d simulation; the z dimension is -simply ignored. -

    -
    - -

    The iso, aniso, and tri keywords are simply shortcuts that are -equivalent to specifying several other keywords together. -

    -

    The keyword iso means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Ptarget" is the same as specifying -these 4 keywords: -

    -
    x Ptarget
-y Ptarget
-z Ptarget
-couple xyz 
-
    -

    The keyword aniso means x, y, and z dimensions are controlled -independently using the Pxx, Pyy, and Pzz components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Ptarget" is the same as specifying these 4 -keywords: -

    -
    x Ptarget
-y Ptarget
-z Ptarget
-couple none 
-
    -

    The keyword tri means x, y, z, xy, xz, and yz dimensions -are controlled independently using their individual stress components -as the driving forces, and the specified scalar pressure as the -external normal stress. Using "tri Ptarget" is the same as specifying -these 7 keywords: -

    -
    x Ptarget
-y Ptarget
-z Ptarget
-xy 0.0 
-yz 0.0 
-xz 0.0 
-couple none 
-
    -
    - -

    The vmax keyword can be used to limit the fractional change in the -volume of the simulation box that can occur in one iteration of the -minimizer. If the pressure is not settling down during the -minimization this can be because the volume is fluctuating too much. -The specified fraction must be greater than 0.0 and should be << 1.0. -A value of 0.001 means the volume cannot change by more than 1/10 of a -percent in one iteration when couple xyz has been specified. For -any other case it means no linear dimension of the simulation box can -change by more than 1/10 of a percent. -

    -
    - -

    With this fix, the potential energy used by the minimizer is augmented -by an additional energy provided by the fix. The overall objective -function then is: -

    -
    -
    -

    where U is the system potential energy, P_t is the desired -hydrostatic pressure, V and V_0 are the system and reference -volumes, respectively. E_strain is the strain energy expression -proposed by Parrinello and Rahman (Parrinello1981). -Taking derivatives of E w.r.t. the box dimensions, and setting these -to zero, we find that at the minimum of the objective function, the -global system stress tensor P will satisfy the relation: -

    -
    -
    -

    where I is the identity matrix, h_0 is the box dimension tensor of -the reference cell, and h_0d is the diagonal part of -h_0. S_t is a symmetric stress tensor that is chosen by LAMMPS -so that the upper-triangular components of P equal the stress tensor -specified by the user. -

    -

    This equation only applies when the box dimensions are equal to those -of the reference dimensions. If this is not the case, then the -converged stress tensor will not equal that specified by the user. We -can resolve this problem by periodically resetting the reference -dimensions. The keyword nreset_ref controls how often this is done. -If this keyword is not used, or is given a value of zero, then the -reference dimensions are set to those of the initial simulation domain -and are never changed. A value of nstep means that every nstep -minimization steps, the reference dimensions are set to those of the -current simulation domain. Note that resetting the reference -dimensions changes the objective function and gradients, which -sometimes causes the minimization to fail. This can be resolved by -changing the value of nreset, or simply continuing the minimization -from a restart file. -

    -

    IMPORTANT NOTE: As normally computed, pressure includes a kinetic- -energy or temperature-dependent component; see the compute -pressure command. However, atom velocities are -ignored during a minimization, and the applied pressure(s) specified -with this command are assumed to only be the virial component of the -pressure (the non-kinetic portion). Thus if atoms have a non-zero -temperature and you print the usual thermodynamic pressure, it may not -appear the system is converging to your specified pressure. The -solution for this is to either (a) zero the velocities of all atoms -before performing the minimization, or (b) make sure you are -monitoring the pressure without its kinetic component. The latter can -be done by outputting the pressure from the fix this command creates -(see below) or a pressure fix you define yourself. -

    -

    IMPORTANT NOTE: Because pressure is often a very sensitive function of -volume, it can be difficult for the minimizer to equilibrate the -system the desired pressure with high precision, particularly for -solids. Some techniques that seem to help are (a) use the -"min_modify line quadratic" option when minimizing with box -relaxations, (b) minimize several times in succession if need be, -to drive the pressure closer to the target pressure, (c) relax -the atom positions before relaxing the box, and (d) relax the box -to the target hydrostatic pressure before relaxing to a target -shear stress state. Also note that -some systems (e.g. liquids) will not sustain a non-hydrostatic applied -pressure, which means the minimizer will not converge. -

    -
    - -

    This fix computes a temperature and pressure each timestep. The -temperature is used to compute the kinetic contribution to the -pressure, even though this is subsequently ignored by default. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if these commands had been issued: -

    -
    compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp virial 
-
    -

    See the compute temp and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is the same -as the fix group. Also note that the pressure compute does not -include a kinetic component. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify temp and press options are -supported by this fix. You can use them to assign a -compute you have defined to this fix which will be used -in its temperature and pressure calculation, as described above. Note -that as described above, if you assign a pressure compute to this fix -that includes a kinetic energy component it will affect the -minimization, most likely in an undesirable way. -

    -

    IMPORTANT NOTE: If both the temp and press keywords are used in a -single thermo_modify command (or in two separate commands), then the -order in which the keywords are specified is important. Note that a -pressure compute defines its own temperature -compute as an argument when it is specified. The temp keyword will -override this (for the pressure compute being used by fix npt), but -only if the temp keyword comes after the press keyword. If the -temp keyword comes before the press keyword, then the new pressure -compute specified by the press keyword will be unaffected by the -temp setting. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -pressure-volume energy, plus the strain energy, if it exists. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    This fix is invoked during energy minimization, but -not for the purpose of adding a contribution to the energy or forces -being minimized. Instead it alters the simulation box geometry as -described above. -

    -

    Restrictions: -

    -

    Only dimensions that are available can be adjusted by this fix. -Non-periodic dimensions are not available. z, xz, and yz, are -not available for 2D simulations. xy, xz, and yz are only -available if the simulation domain is non-orthogonal. The -create_box, read data, and -read_restart commands specify whether the -simulation box is orthogonal or non-orthogonal (triclinic) and explain -the meaning of the xy,xz,yz tilt factors. -

    -

    The scaleyz yes and scalexz yes keyword/value pairs can not be used -for 2D simulations. scaleyz yes, scalexz yes, and scalexy yes options -can only be used if the 2nd dimension in the keyword is periodic, -and if the tilt factor is not coupled to the barostat via keywords -tri, yz, xz, and xy. -

    -

    Related commands: -

    -

    fix npt, minimize -

    -

    Default: -

    -

    The keyword defaults are dilate = all, vmax = 0.0001, nreset = 0. -

    -
    - - - -

    (Parrinello1981) Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). -

    - diff --git a/doc/doc2/fix_colvars.html b/doc/doc2/fix_colvars.html deleted file mode 100644 index 5aa30bb707..0000000000 --- a/doc/doc2/fix_colvars.html +++ /dev/null @@ -1,147 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix colvars command -

    -

    Syntax: -

    -
    fix ID group-ID colvars configfile keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • colvars = style name of this fix command - -
    • configfile = the configuration file for the colvars module - -
    • keyword = input or output or seed or tstat - -
        input arg = colvars.state file name or prefix or NULL (default: NULL)
-  output arg = output filename prefix (default: out)
-  seed arg = seed for random number generator (default: 1966)
-  unwrap arg = yes or no
-    use unwrapped coordinates in collective variables (default: yes)
-  tstat arg = fix id of a thermostat or NULL (default: NULL) 
-
      - -
    -

    Examples: -

    -
    fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
-fix abf all colvars colvars.inp tstat 1 
-
    -

    Description: -

    -

    This fix interfaces LAMMPS to a "collective variables" or "colvars" -module library which allows to calculate potentials of mean force -(PMFs) for any set of colvars, using different sampling methods: -currently implemented are the Adaptive Biasing Force (ABF) method, -metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling -(US) via a flexible harmonic restraint bias. The colvars library is -hosted at http://colvars.github.io/ -

    -

    This documentation describes only the fix colvars command itself and -LAMMPS specific parts of the code. The full documentation of the -colvars library is available as this supplementary PDF document -

    -

    A detailed discussion of the implementation of the portable collective -variable library is in (Fiorin). Additional information can -be found in (Henin). -

    -

    There are some example scripts for using this package with LAMMPS in the -examples/USER/colvars directory. -

    -
    - -

    The only mandatory argument to the fix is the filename to the colvars -input file that contains the input that is independent from the MD -program in which the colvars library has been integrated. -

    -

    The group-ID entry is ignored. The collective variable module will -always apply to the entire system and there can only be one instance -of the colvars fix at a time. The colvars fix will only communicate -the minimum information necessary and the colvars library supports -multiple, completely independent collective variables, so there is -no restriction to functionaliry by limiting the number of colvars fixes. -

    -

    The input keyword allows to specify a state file that would contain -the restart information required in order to continue a calculation from -a prerecorded state. Fix colvars records it state in binary restart -files, so when using the read_restart command, -this is usually not needed. -

    -

    The output keyword allows to specify the output prefix. All output -files generated will use this prefix followed by the ".colvars." and -a word like "state" or "traj". -

    -

    The seed keyword contains the seed for the random number generator -that will be used in the colvars module. -

    -

    The unwrap keyword controls whether wrapped or unwrapped coordinates -are passed to the colvars library for calculation of the collective -variables and the resulting forces. The default is yes, i.e. to use -the image flags to reconstruct the absolute atom positions. -Setting this to no will use the current local coordinates that are -wrapped back into the simulation cell at each re-neighboring instead. -

    -

    The tstat keyword can be either NULL or the label of a thermostating -fix that thermostats all atoms in the fix colvars group. This will be -used to provide the colvars module with the current thermostat target -temperature. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the current status of the colvars module into -binary restart files. This is in addition to the text -mode status file that is written by the colvars module itself and the -kind of information in both files is identical. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change from the biasing force added by the fix -to the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". -

    -

    Restrictions: -

    -

    This fix is part of the USER-COLVARS package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    There can only be one colvars fix active at a time. Since the interface -communicates only the minimum amount of information and colvars module -itself can handle an arbitrary number of collective variables, this is -not a limitation of functionality. -

    -

    Related commands: -

    -

    fix smd -

    -

    Default: -

    -

    The default options are input = NULL, output = out, seed = 1966, unwrap yes, -and tstat = NULL. -

    -
    - - - -

    (Fiorin) Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 -

    - - -

    (Henin) Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, -35-47 (2010) -

    - diff --git a/doc/doc2/fix_deform.html b/doc/doc2/fix_deform.html deleted file mode 100644 index b529bfae4a..0000000000 --- a/doc/doc2/fix_deform.html +++ /dev/null @@ -1,607 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix deform command -

    -

    fix deform/kk command -

    -

    Syntax: -

    -
    fix ID group-ID deform N parameter args ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • deform = style name of this fix command - -
    • N = perform box deformation every this many timesteps - -
    • one or more parameter/arg pairs may be appended - -
      parameter = x or y or z or xy or xz or yz
-  x, y, z args = style value(s)
-    style = final or delta or scale or vel or erate or trate or volume or wiggle or variable
-      final values = lo hi
-        lo hi = box boundaries at end of run (distance units)
-      delta values = dlo dhi
-        dlo dhi = change in box boundaries at end of run (distance units)
-      scale values = factor
-        factor = multiplicative factor for change in box length at end of run
-      vel value = V
-        V = change box length at this velocity (distance/time units),
-	    effectively an engineering strain rate
-      erate value = R
-        R = engineering strain rate (1/time units)
-      trate value = R
-        R = true strain rate (1/time units)
-      volume value = none = adjust this dim to preserve volume of system
-      wiggle values = A Tp
-        A = amplitude of oscillation (distance units)
-	Tp = period of oscillation (time units)
-      variable values = v_name1 v_name2
-        v_name1 = variable with name1 for box length change as function of time
-	v_name2 = variable with name2 for change rate as function of time
-  xy, xz, yz args = style value
-    style = final or delta or vel or erate or trate or wiggle
-      final value = tilt
-        tilt = tilt factor at end of run (distance units)
-      delta value = dtilt
-        dtilt = change in tilt factor at end of run (distance units)
-      vel value = V
-        V = change tilt factor at this velocity (distance/time units),
-	    effectively an engineering shear strain rate
-      erate value = R
-        R = engineering shear strain rate (1/time units)
-      trate value = R
-        R = true shear strain rate (1/time units)
-      wiggle values = A Tp
-        A = amplitude of oscillation (distance units)
-	Tp = period of oscillation (time units)
-      variable values = v_name1 v_name2
-        v_name1 = variable with name1 for tilt change as function of time
-	v_name2 = variable with name2 for change rate as function of time 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = remap or flip or units - -
        remap value = x or v or none
-    x = remap coords of atoms in group into deforming box
-    v = remap velocities of all atoms when they cross periodic boundaries
-    none = no remapping of x or v
-  flip value = yes or no
-    allow or disallow box flips when it becomes highly skewed
-  units value = lattice or box
-    lattice = distances are defined in lattice units
-    box = distances are defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box
-fix 1 all deform 1 x trate 0.1 y volume z volume
-fix 1 all deform 1 xy erate 0.001 remap v
-fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0 
-
    -

    Description: -

    -

    Change the volume and/or shape of the simulation box during a dynamics -run. Orthogonal simulation boxes have 3 adjustable parameters -(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 -adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be -adjusted independently and simultaneously by this command. This fix -can be used to perform non-equilibrium MD (NEMD) simulations of a -continuously strained system. See the fix -nvt/sllod and compute -temp/deform commands for more details. -

    -

    For the x, y, z parameters, the associated dimension cannot be -shrink-wrapped. For the xy, yz, xz parameters, the associated -2nd dimension cannot be shrink-wrapped. Dimensions not varied by this -command can be periodic or non-periodic. Dimensions corresponding to -unspecified parameters can also be controlled by a fix -npt or fix nph command. -

    -

    The size and shape of the simulation box at the beginning of the -simulation run were either specified by the -create_box or read_data or -read_restart command used to setup the simulation -initially if it is the first run, or they are the values from the end -of the previous run. The create_box, read -data, and read_restart commands -specify whether the simulation box is orthogonal or non-orthogonal -(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If -fix deform changes the xy,xz,yz tilt factors, then the simulation box -must be triclinic, even if its initial tilt factors are 0.0. -

    -

    As described below, the desired simulation box size and shape at the -end of the run are determined by the parameters of the fix deform -command. Every Nth timestep during the run, the simulation box is -expanded, contracted, or tilted to ramped values between the initial -and final values. -

    -
    - -

    For the x, y, and z parameters, this is the meaning of their -styles and values. -

    -

    The final, delta, scale, vel, and erate styles all change -the specified dimension of the box via "constant displacement" which -is effectively a "constant engineering strain rate". This means the -box dimension changes linearly with time from its initial to final -value. -

    -

    For style final, the final lo and hi box boundaries of a dimension -are specified. The values can be in lattice or box distance units. -See the discussion of the units keyword below. -

    -

    For style delta, plus or minus changes in the lo/hi box boundaries -of a dimension are specified. The values can be in lattice or box -distance units. See the discussion of the units keyword below. -

    -

    For style scale, a multiplicative factor to apply to the box length -of a dimension is specified. For example, if the initial box length -is 10, and the factor is 1.1, then the final box length will be 11. A -factor less than 1.0 means compression. -

    -

    For style vel, a velocity at which the box length changes is -specified in units of distance/time. This is effectively a "constant -engineering strain rate", where rate = V/L0 and L0 is the initial box -length. The distance can be in lattice or box distance units. See -the discussion of the units keyword below. For example, if the -initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then -after 10 psec, the box length will have doubled. After 20 psec, it -will have tripled. -

    -

    The erate style changes a dimension of the the box at a "constant -engineering strain rate". The units of the specified strain rate are -1/time. See the units command for the time units -associated with different choices of simulation units, -e.g. picoseconds for "metal" units). Tensile strain is unitless and -is defined as delta/L0, where L0 is the original box length and delta -is the change relative to the original length. The box length L as a -function of time will change as -

    -
    L(t) = L0 (1 + erate*dt) 
-
    -

    where dt is the elapsed time (in time units). Thus if erate R is -specified as 0.1 and time units are picoseconds, this means the box -length will increase by 10% of its original length every picosecond. -I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc. R = --0.01 means the box length will shrink by 1% of its original length -every picosecond. Note that for an "engineering" rate the change is -based on the original box length, so running with R = 1 for 10 -picoseconds expands the box length by a factor of 11 (strain of 10), -which is different that what the trate style would induce. -

    -

    The trate style changes a dimension of the box at a "constant true -strain rate". Note that this is not an "engineering strain rate", as -the other styles are. Rather, for a "true" rate, the rate of change -is constant, which means the box dimension changes non-linearly with -time from its initial to final value. The units of the specified -strain rate are 1/time. See the units command for the -time units associated with different choices of simulation units, -e.g. picoseconds for "metal" units). Tensile strain is unitless and -is defined as delta/L0, where L0 is the original box length and delta -is the change relative to the original length. -

    -

    The box length L as a function of time will change as -

    -
    L(t) = L0 exp(trate*dt) 
-
    -

    where dt is the elapsed time (in time units). Thus if trate R is -specified as ln(1.1) and time units are picoseconds, this means the -box length will increase by 10% of its current (not original) length -every picosecond. I.e. strain after 1 psec = 0.1, strain after 2 psec -= 0.21, etc. R = ln(2) or ln(3) means the box length will double or -triple every picosecond. R = ln(0.99) means the box length will -shrink by 1% of its current length every picosecond. Note that for a -"true" rate the change is continuous and based on the current length, -so running with R = ln(2) for 10 picoseconds does not expand the box -length by a factor of 11 as it would with erate, but by a factor of -1024 since the box length will double every picosecond. -

    -

    Note that to change the volume (or cross-sectional area) of the -simulation box at a constant rate, you can change multiple dimensions -via erate or trate. E.g. to double the box volume in a picosecond -picosecond, you could set "x erate M", "y erate M", "z erate M", with -M = pow(2,1/3) - 1 = 0.26, since if each box dimension grows by 26%, -the box volume doubles. Or you could set "x trate M", "y trate M", "z -trate M", with M = ln(1.26) = 0.231, and the box volume would double -every picosecond. -

    -

    The volume style changes the specified dimension in such a way that -the box volume remains constant while other box dimensions are changed -explicitly via the styles discussed above. For example, "x scale 1.1 -y scale 1.1 z volume" will shrink the z box length as the x,y box -lengths increase, to keep the volume constant (product of x,y,z -lengths). If "x scale 1.1 z volume" is specified and parameter y is -unspecified, then the z box length will shrink as x increases to keep -the product of x,z lengths constant. If "x scale 1.1 y volume z -volume" is specified, then both the y,z box lengths will shrink as x -increases to keep the volume constant (product of x,y,z lengths). In -this case, the y,z box lengths shrink so as to keep their relative -aspect ratio constant. -

    -

    For solids or liquids, note that when one dimension of the box is -expanded via fix deform (i.e. tensile strain), it may be physically -undesirable to hold the other 2 box lengths constant (unspecified by -fix deform) since that implies a density change. Using the volume -style for those 2 dimensions to keep the box volume constant may make -more physical sense, but may also not be correct for materials and -potentials whose Poisson ratio is not 0.5. An alternative is to use -fix npt aniso with zero applied pressure on those 2 -dimensions, so that they respond to the tensile strain dynamically. -

    -

    The wiggle style oscillates the specified box length dimension -sinusoidally with the specified amplitude and period. I.e. the box -length L as a function of time is given by -

    -
    L(t) = L0 + A sin(2*pi t/Tp) 
-
    -

    where L0 is its initial length. If the amplitude A is a positive -number the box initially expands, then contracts, etc. If A is -negative then the box initially contracts, then expands, etc. The -amplitude can be in lattice or box distance units. See the discussion -of the units keyword below. -

    -

    The variable style changes the specified box length dimension by -evaluating a variable, which presumably is a function of time. The -variable with name1 must be an equal-style variable -and should calculate a change in box length in units of distance. -Note that this distance is in box units, not lattice units; see the -discussion of the units keyword below. The formula associated with -variable name1 can reference the current timestep. Note that it -should return the "change" in box length, not the absolute box length. -This means it should evaluate to 0.0 when invoked on the initial -timestep of the run following the definition of fix deform. It should -evaluate to a value > 0.0 to dilate the box at future times, or a -value < 0.0 to compress the box. -

    -

    The variable name2 must also be an equal-style -variable and should calculate the rate of box length -change, in units of distance/time, i.e. the time-derivative of the -name1 variable. This quantity is used internally by LAMMPS to reset -atom velocities when they cross periodic boundaries. It is computed -internally for the other styles, but you must provide it when using an -arbitrary variable. -

    -

    Here is an example of using the variable style to perform the same -box deformation as the wiggle style formula listed above, where we -assume that the current timestep = 0. -

    -
    variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 x variable v_displace v_rate remap v 
-
    -

    For the scale, vel, erate, trate, volume, wiggle, and -variable styles, the box length is expanded or compressed around its -mid point. -

    -
    - -

    For the xy, xz, and yz parameters, this is the meaning of their -styles and values. Note that changing the tilt factors of a triclinic -box does not change its volume. -

    -

    The final, delta, vel, and erate styles all change the shear -strain at a "constant engineering shear strain rate". This means the -tilt factor changes linearly with time from its initial to final -value. -

    -

    For style final, the final tilt factor is specified. The value -can be in lattice or box distance units. See the discussion of the -units keyword below. -

    -

    For style delta, a plus or minus change in the tilt factor is -specified. The value can be in lattice or box distance units. See -the discussion of the units keyword below. -

    -

    For style vel, a velocity at which the tilt factor changes is -specified in units of distance/time. This is effectively an -"engineering shear strain rate", where rate = V/L0 and L0 is the -initial box length perpendicular to the direction of shear. The -distance can be in lattice or box distance units. See the discussion -of the units keyword below. For example, if the initial tilt factor -is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the -tilt factor will be 15 Angstroms. After 2 psec, it will be 25 -Angstroms. -

    -

    The erate style changes a tilt factor at a "constant engineering -shear strain rate". The units of the specified shear strain rate are -1/time. See the units command for the time units -associated with different choices of simulation units, -e.g. picoseconds for "metal" units). Shear strain is unitless and is -defined as offset/length, where length is the box length perpendicular -to the shear direction (e.g. y box length for xy deformation) and -offset is the displacement distance in the shear direction (e.g. x -direction for xy deformation) from the unstrained orientation. -

    -

    The tilt factor T as a function of time will change as -

    -
    T(t) = T0 + L0*erate*dt 
-
    -

    where T0 is the initial tilt factor, L0 is the original length of the -box perpendicular to the shear direction (e.g. y box length for xy -deformation), and dt is the elapsed time (in time units). Thus if -erate R is specified as 0.1 and time units are picoseconds, this -means the shear strain will increase by 0.1 every picosecond. I.e. if -the xy shear strain was initially 0.0, then strain after 1 psec = 0.1, -strain after 2 psec = 0.2, etc. Thus the tilt factor would be 0.0 at -time 0, 0.1*ybox at 1 psec, 0.2*ybox at 2 psec, etc, where ybox is the -original y box length. R = 1 or 2 means the tilt factor will increase -by 1 or 2 every picosecond. R = -0.01 means a decrease in shear -strain by 0.01 every picosecond. -

    -

    The trate style changes a tilt factor at a "constant true shear -strain rate". Note that this is not an "engineering shear strain -rate", as the other styles are. Rather, for a "true" rate, the rate -of change is constant, which means the tilt factor changes -non-linearly with time from its initial to final value. The units of -the specified shear strain rate are 1/time. See the -units command for the time units associated with -different choices of simulation units, e.g. picoseconds for "metal" -units). Shear strain is unitless and is defined as offset/length, -where length is the box length perpendicular to the shear direction -(e.g. y box length for xy deformation) and offset is the displacement -distance in the shear direction (e.g. x direction for xy deformation) -from the unstrained orientation. -

    -

    The tilt factor T as a function of time will change as -

    -
    T(t) = T0 exp(trate*dt) 
-
    -

    where T0 is the initial tilt factor and dt is the elapsed time (in -time units). Thus if trate R is specified as ln(1.1) and time units -are picoseconds, this means the shear strain or tilt factor will -increase by 10% every picosecond. I.e. if the xy shear strain was -initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec = -0.121, etc. R = ln(2) or ln(3) means the tilt factor will double or -triple every picosecond. R = ln(0.99) means the tilt factor will -shrink by 1% every picosecond. Note that the change is continuous, so -running with R = ln(2) for 10 picoseconds does not change the tilt -factor by a factor of 10, but by a factor of 1024 since it doubles -every picosecond. Note that the initial tilt factor must be non-zero -to use the trate option. -

    -

    Note that shear strain is defined as the tilt factor divided by the -perpendicular box length. The erate and trate styles control the -tilt factor, but assume the perpendicular box length remains constant. -If this is not the case (e.g. it changes due to another fix deform -parameter), then this effect on the shear strain is ignored. -

    -

    The wiggle style oscillates the specified tilt factor sinusoidally -with the specified amplitude and period. I.e. the tilt factor T as a -function of time is given by -

    -
    T(t) = T0 + A sin(2*pi t/Tp) 
-
    -

    where T0 is its initial value. If the amplitude A is a positive -number the tilt factor initially becomes more positive, then more -negative, etc. If A is negative then the tilt factor initially -becomes more negative, then more positive, etc. The amplitude can be -in lattice or box distance units. See the discussion of the units -keyword below. -

    -

    The variable style changes the specified tilt factor by evaluating a -variable, which presumably is a function of time. The variable with -name1 must be an equal-style variable and should -calculate a change in tilt in units of distance. Note that this -distance is in box units, not lattice units; see the discussion of the -units keyword below. The formula associated with variable name1 -can reference the current timestep. Note that it should return the -"change" in tilt factor, not the absolute tilt factor. This means it -should evaluate to 0.0 when invoked on the initial timestep of the run -following the definition of fix deform. -

    -

    The variable name2 must also be an equal-style -variable and should calculate the rate of tilt change, -in units of distance/time, i.e. the time-derivative of the name1 -variable. This quantity is used internally by LAMMPS to reset atom -velocities when they cross periodic boundaries. It is computed -internally for the other styles, but you must provide it when using an -arbitrary variable. -

    -

    Here is an example of using the variable style to perform the same -box deformation as the wiggle style formula listed above, where we -assume that the current timestep = 0. -

    -
    variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 xy variable v_displace v_rate remap v 
-
    -
    - -

    All of the tilt styles change the xy, xz, yz tilt factors during a -simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes -are normally bounded by half the distance of the parallel box length. -See the discussion of the flip keyword below, to allow this bound to -be exceeded, if desired. -

    -

    For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all equivalent. -

    -

    To obey this constraint and allow for large shear deformations to be -applied via the xy, xz, or yz parameters, the following -algorithm is used. If prd is the associated parallel box length (10 -in the example above), then if the tilt factor exceeds the accepted -range of -5 to 5 during the simulation, then the box is flipped to the -other limit (an equivalent box) and the simulation continues. Thus -for this example, if the initial xy tilt factor was 0.0 and "xy final -100.0" was specified, then during the simulation the xy tilt factor -would increase from 0.0 to 5.0, the box would be flipped so that the -tilt factor becomes -5.0, the tilt factor would increase from -5.0 to -5.0, the box would be flipped again, etc. The flip occurs 10 times -and the final tilt factor at the end of the simulation would be 0.0. -During each flip event, atoms are remapped into the new box in the -appropriate manner. -

    -

    The one exception to this rule is if the 1st dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient due to the highly skewed simulation box. -

    -
    - -

    Each time the box size or shape is changed, the remap keyword -determines whether atom positions are remapped to the new box. If -remap is set to x (the default), atoms in the fix group are -remapped; otherwise they are not. Note that their velocities are not -changed, just their positions are altered. If remap is set to v, -then any atom in the fix group that crosses a periodic boundary will -have a delta added to its velocity equal to the difference in -velocities between the lo and hi boundaries. Note that this velocity -difference can include tilt components, e.g. a delta in the x velocity -when an atom crosses the y periodic boundary. If remap is set to -none, then neither of these remappings take place. -

    -

    Conceptually, setting remap to x forces the atoms to deform via an -affine transformation that exactly matches the box deformation. This -setting is typically appropriate for solids. Note that though the -atoms are effectively "moving" with the box over time, it is not due -to their having a velocity that tracks the box change, but only due to -the remapping. By contrast, setting remap to v is typically -appropriate for fluids, where you want the atoms to respond to the -change in box size/shape on their own and acquire a velocity that -matches the box change, so that their motion will naturally track the -box without explicit remapping of their coordinates. -

    -

    IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are -performed using this fix, the option "remap v" should normally be -used. This is because fix nvt/sllod adjusts the -atom positions and velocities to induce a velocity profile that -matches the changing box size/shape. Thus atom coordinates should NOT -be remapped by fix deform, but velocities SHOULD be when atoms cross -periodic boundaries, since that is consistent with maintaining the -velocity profile already created by fix nvt/sllod. LAMMPS will warn -you if the remap setting is not consistent with fix nvt/sllod. -

    -

    IMPORTANT NOTE: For non-equilibrium MD (NEMD) simulations using "remap -v" it is usually desirable that the fluid (or flowing material, -e.g. granular particles) stream with a velocity profile consistent -with the deforming box. As mentioned above, using a thermostat such -as fix nvt/sllod or fix -lavgevin (with a bias provided by compute -temp/deform), will typically accomplish -that. If you do not use a thermostat, then there is no driving force -pushing the atoms to flow in a manner consistent with the deforming -box. E.g. for a shearing system the box deformation velocity may vary -from 0 at the bottom to 10 at the top of the box. But the stream -velocity profile of the atoms may vary from -5 at the bottom to +5 at -the top. You can monitor these effects using the fix -ave/spatial, compute -temp/deform, and compute -temp/profile commands. One way to induce -atoms to stream consistent with the box deformation is to give them an -initial velocity profile, via the velocity ramp -command, that matches the box deformation rate. This also typically -helps the system come to equilibrium more quickly, even if a -thermostat is used. -

    -

    IMPORTANT NOTE: If a fix rigid is defined for rigid -bodies, and remap is set to x, then the center-of-mass coordinates -of rigid bodies will be remapped to the changing simulation box. This -will be done regardless of whether atoms in the rigid bodies are in -the fix deform group or not. The velocity of the centers of mass are -not remapped even if remap is set to v, since fix -nvt/sllod does not currently do anything special -for rigid particles. If you wish to perform a NEMD simulation of -rigid particles, you can either thermostat them independently or -include a background fluid and thermostat the fluid via fix -nvt/sllod. -

    -

    The flip keyword allows the tilt factors for a triclinic box to -exceed half the distance of the parallel box length, as discussed -above. If the flip value is set to yes, the bound is enforced by -flipping the box when it is exceeded. If the flip value is set to -no, the tilt will continue to change without flipping. Note that if -you apply large deformations, this means the box shape can tilt -dramatically LAMMPS will run less efficiently, due to the large volume -of communication needed to acquire ghost atoms around a processor's -irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may -also lose atoms and generate an error. -

    -

    The units keyword determines the meaning of the distance units used -to define various arguments. A box value selects standard distance -units as defined by the units command, e.g. Angstroms for -units = real or metal. A lattice value means the distance units are -in lattice spacings. The lattice command must have -been previously used to define the lattice spacing. Note that the -units choice also affects the vel style parameters since it is -defined in terms of distance/time. Also note that the units keyword -does not affect the variable style. You should use the xlat, -ylat, zlat keywords of the thermo_style -command if you want to include lattice spacings in a variable formula. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. -

    -

    This fix can perform deformation over multiple runs, using the start -and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    You cannot apply x, y, or z deformations to a dimension that is -shrink-wrapped via the boundary comamnd. -

    -

    You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in -xy) that is shrink-wrapped via the boundary comamnd. -

    -

    Related commands: -

    -

    change_box -

    -

    Default: -

    -

    The option defaults are remap = x, flip = yes, and units = lattice. -

    - diff --git a/doc/doc2/fix_deposit.html b/doc/doc2/fix_deposit.html deleted file mode 100644 index 93a498194a..0000000000 --- a/doc/doc2/fix_deposit.html +++ /dev/null @@ -1,292 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix deposit command -

    -

    Syntax: -

    -
    fix ID group-ID deposit N type M seed keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • deposit = style name of this fix command - -
    • N = # of atoms or molecules to insert - -
    • type = atom type to assign to inserted atoms (offset for moleclue insertion) - -
    • M = insert a single atom or molecule every M steps - -
    • seed = random # seed (positive integer) - -
    • one or more keyword/value pairs may be appended to args - -
    • keyword = region or id or global or local or near or attempt or rate or vx or vy or vz or mol or rigid or shake or units - -
        region value = region-ID
-    region-ID = ID of region to use as insertion volume
-  id value = max or next
-    max = atom ID for new atom(s) is max ID of all current atoms plus one
-    next = atom ID for new atom(s) increments by one for every deposition
-  global values = lo hi
-    lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
-  local values = lo hi delta
-    lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
-    delta = lateral distance within which a neighbor is considered "nearby" (distance units)
-  near value = R
-    R = only insert atom/molecule if further than R from existing particles (distance units)
-  attempt value = Q
-    Q = attempt a single insertion up to Q times
-  rate value = V
-    V = z velocity (y in 2d) at which insertion volume moves (velocity units)
-  vx values = vxlo vxhi
-    vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
-  vy values = vylo vyhi
-    vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
-  vz values = vzlo vzhi
-    vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
-  target values = tx ty tz
-    tx,ty,tz = location of target point (distance units)
-  mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
-  molfrac values = f1 f2 ... fN
-    f1 to fN = relative probability of creating each of N molecules in template-ID
-  rigid value = fix-ID
-    fix-ID = ID of fix rigid/small command
-  shake value = fix-ID
-    fix-ID = ID of fix shake command
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
-fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
-fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice 
-
    -

    Description: -

    -

    Insert a single atom or molecule into the simulation domain every M -timesteps until N atoms or molecules have been inserted. This is -useful for simulating deposition onto a surface. For the remainder of -this doc page, a single inserted atom or molecule is referred to as a -"particle". -

    -

    If inserted particles are individual atoms, they are assigned the -specified atom type. If they are molecules, the type of each atom in -the inserted molecule is specified in the file read by the -molecule command, and those values are added to the -specified atom type. E.g. if the file specifies atom types 1,2,3, and -those are the atom types you want for inserted molecules, then specify -type = 0. If you specify type = 2, the in the inserted molecule -will have atom types 3,4,5. -

    -

    All atoms in the inserted particle are assigned to two groups: the -default group "all" and the group specified in the fix deposit command -(which can also be "all"). -

    -

    If you are computing temperature values which include inserted -particles, you will want to use the -compute_modify dynamic option, which insures the -current number of atoms is used as a normalizing factor each time the -temperature is computed. -

    -

    Care must be taken that inserted particles are not too near existing -atoms, using the options described below. When inserting particles -above a surface in a non-periodic box (see the -boundary command), the possibility of a particle -escaping the surface and flying upward should be considered, since the -particle may be lost or the box size may grow infinitely large. A -fix wall/reflect command can be used to -prevent this behavior. Note that if a shrink-wrap boundary is used, -it is OK to insert the new particle outside the box, however the box -will immediately be expanded to include the new particle. When -simulating a sputtering experiment it is probably more realistic to -ignore those atoms using the thermo_modify -command with the lost ignore option and a fixed -boundary. -

    -

    The fix deposit command must use the region keyword to define an -insertion volume. The specified region must have been previously -defined with a region command. It must be defined with -side = in. -

    -

    IMPORTANT NOTE: LAMMPS checks that the specified region is wholly -inside the simulation box. It can do this correctly for orthonormal -simulation boxes. However for triclinic -boxes, it only tests against the larger -orthonormal box that bounds the tilted simulation box. If the -specified region includes volume outside the tilted box, then an -insertion will likely fail, leading to a "lost atoms" error. Thus for -triclinic boxes you should insure the specified region is wholly -inside the simulation box. -

    -

    Individual atoms are inserted, unless the mol keyword is used. It -specifies a template-ID previously defined using the -molecule command, which reads files that define one or -more molecules. The coordinates, atom types, charges, etc, as well as -any bond/angle/etc and special neighbor information for the molecule -can be specified in the molecule file. See the -molecule command for details. The only settings -required to be in each file are the coordinates and types of atoms in -the molecule. -

    -

    If the molecule template contains more than one molecule, the relative -probability of depositing each molecule can be specified by the -molfrac keyword. N relative probablities, each from 0.0 to 1.0, are -specified, where N is the number of molecules in the template. Each -time a molecule is deposited, a random number is used to sample from -the list of relative probabilities. The N values must sum to 1.0. -

    -

    If you wish to insert molecules via the mol keyword, that will be -treated as rigid bodies, use the rigid keyword, specifying as its -value the ID of a separate fix rigid/small -command which also appears in your input script. -

    -

    If you wish to insert molecules via the mol keyword, that will have -their bonds or angles constrained via SHAKE, use the shake keyword, -specifying as its value the ID of a separate fix -shake command which also appears in your input script. -

    -

    Each timestep a particle is inserted, the coordinates for its atoms -are chosen as follows. For insertion of individual atoms, the -"position" referred to in the following description is the coordinate -of the atom. For insertion of molecule, the "position" is the -geometric center of the molecule; see the molecule doc -page for details. A random rotation of the molecule around its center -point is performed, which determines the coordinates all the -individual atoms. -

    -

    A random position within the region insertion volume is generated. If -neither the global or local keyword is used, the random position -is the trial position. If the global keyword is used, the random -x,y values are used, but the z position of the new particle is set -above the highest current atom in the simulation by a distance -randomly chosen between lo/hi. (For a 2d simulation, this is done for -the y position.) If the local keyword is used, the z position is -set a distance between lo/hi above the highest current atom in the -simulation that is "nearby" the chosen x,y position. In this context, -"nearby" means the lateral distance (in x,y) between the new and old -particles is less than the delta setting. -

    -

    Once a trial x,y,z position has been selected, the insertion is only -performed if no current atom in the simulation is within a distance R -of any atom in the new particle, including the effect of periodic -boundary conditions if applicable. R is defined by the near -keyword. Note that the default value for R is 0.0, which will allow -atoms to strongly overlap if you are inserting where other atoms are -present. This distance test is performed independently for each atom -in an inserted molecule, based on the randomly rotated configuration -of the molecule. If this test fails, a new random position within the -insertion volume is chosen and another trial is made. Up to Q -attempts are made. If the particle is not successfully inserted, -LAMMPS prints a warning message. -

    -

    IMPORTANT NOTE: If you are inserting finite size particles or a -molecule or rigid body consisting of finite-size particles, then you -should typically set R larger than the distance at which any inserted -particle may overlap with either a previouly inserted particle or an -existing particle. LAMMPS will issue a warning if R is smaller than -this value, based on the radii of existing and inserted particles. -

    -

    The rate option moves the insertion volume in the z direction (3d) -or y direction (2d). This enables particles to be inserted from a -successively higher height over time. Note that this parameter is -ignored if the global or local keywords are used, since those -options choose a z-coordinate for insertion independently. -

    -

    The vx, vy, and vz components of velocity for the inserted particle -are set using the values specified for the vx, vy, and vz -keywords. Note that normally, new particles should be a assigned a -negative vertical velocity so that they move towards the surface. For -molecules, the same velocity is given to every particle (no rotation -or bond vibration). -

    -

    If the target option is used, the velocity vector of the inserted -particle is changed so that it points from the insertion position -towards the specified target point. The magnitude of the velocity is -unchanged. This can be useful, for example, for simulating a -sputtering process. E.g. the target point can be far away, so that -all incident particles strike the surface as if they are in an -incident beam of particles at a prescribed angle. -

    -

    The id keyword determines how atom IDs and molecule IDs are assigned -to newly deposited particles. Molecule IDs are only assigned if -molecules are being inserted. For the max setting, the atom and -molecule IDs of all current atoms are checked. Atoms in the new -particle are assigned IDs starting with the current maximum plus one. -If a molecule is inserted it is assigned an ID = current maximum plus -one. This means that if particles leave the system, the new IDs may -replace the lost ones. For the next setting, the maximum ID of any -atom and molecule is stored at the time the fix is defined. Each time -a new particle is added, this value is incremented to assign IDs to -the new atom(s) or molecule. Thus atom and molecule IDs for deposited -particles will be consecutive even if particles leave the system over -time. -

    -

    The units keyword determines the meaning of the distance units used -for the other deposition parameters. A box value selects standard -distance units as defined by the units command, -e.g. Angstroms for units = real or metal. A lattice value means the -distance units are in lattice spacings. The lattice -command must have been previously used to define the lattice spacing. -Note that the units choice affects all the keyword values that have -units of distance or velocity. -

    -

    IMPORTANT NOTE: If you are monitoring the temperature of a system -where the atom count is changing due to adding particles, you -typically should use the compute_modify dynamic -yes command for the temperature compute you are -using. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the deposition to binary restart -files. This includes information about how many -particles have been depositied, the random number generator seed, the -next timestep for deposition, etc. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    None of the fix_modify options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various output commands. No -parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    The specified insertion region cannot be a "dynamic" region, as -defined by the region command. -

    -

    Related commands: -

    -

    fix_pour, region -

    -

    Default: -

    -

    Insertions are performed for individual atoms, i.e. no mol setting -is defined. If the mol keyword is used, the default for molfrac -is an equal probabilities for all molecules in the template. -Additional option defaults are id = max, delta = 0.0, near = 0.0, -attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0, -and units = lattice. -

    - diff --git a/doc/doc2/fix_drag.html b/doc/doc2/fix_drag.html deleted file mode 100644 index adef7e6576..0000000000 --- a/doc/doc2/fix_drag.html +++ /dev/null @@ -1,66 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix drag command -

    -

    Syntax: -

    -
    fix ID group-ID drag x y z fmag delta 
-
    -
    • ID, group-ID are documented in fix command -
    • drag = style name of this fix command -
    • x,y,z = coord to drag atoms towards -
    • fmag = magnitude of force to apply to each atom (force units) -
    • delta = cutoff distance inside of which force is not applied (distance units) -
    -

    Examples: -

    -
    fix center small-molecule drag 0.0 10.0 0.0 5.0 2.0 
-
    -

    Description: -

    -

    Apply a force to each atom in a group to drag it towards the point -(x,y,z). The magnitude of the force is specified by fmag. If an atom -is closer than a distance delta to the point, then the force is not -applied. -

    -

    Any of the x,y,z values can be specified as NULL which means do not -include that dimension in the distance calculation or force -application. -

    -

    This command can be used to steer one or more atoms to a new location -in the simulation. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global 3-vector of forces, which can be accessed -by various output commands. This is the -total force on the group of atoms by the drag force. The vector -values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix spring, fix spring/self, -fix spring/rg, fix smd -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_drude.html b/doc/doc2/fix_drude.html deleted file mode 100644 index 398abd701e..0000000000 --- a/doc/doc2/fix_drude.html +++ /dev/null @@ -1,60 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix drude command -

    -

    Syntax: -

    -
    fix ID group-ID drude flag1 flag2 ... flagN 
-
    -
    • ID, group-ID are documented in fix command -
    • drude = style name of this fix command -
    • tag = Drude flag for each atom type (1 to N) in the system -
    -

    Examples: -

    -
    fix 1 all drude 1 1 0 1 0 2 2 2
-fix 1 all drude C C N C N D D D 
-
    -

    Description: -

    -

    Assign each atom type in the system to be one of 3 kinds of atoms -within the Drude polarization model. This compute is designed to be -used with the thermalized Drude oscillator -model. Polarizable models in LAMMPS -are described in this Section. -

    -

    The three possible types can be designated with an integer (0,1,2) -or capital letter (N,C,D): -

    -
    • 0 or N = non-polarizable atom (not part of Drude model) -
    • 1 or C = Drude core -
    • 2 or D = Drude electron -
    -

    Restrictions: -

    -

    This fix should be invoked before any other commands that implement -the Drude oscillator model, such as fix -langevin_drude, fix -drude/transform, compute -temp/drude, pair_style -thole. -

    -

    Related commands: -

    -

    fix langevin_drude, fix -drude/transform, compute -temp/drude, pair_style -thole -

    -

    Default: None -

    - diff --git a/doc/doc2/fix_drude_transform.html b/doc/doc2/fix_drude_transform.html deleted file mode 100644 index f19e5df09c..0000000000 --- a/doc/doc2/fix_drude_transform.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix drude/transform/direct command -

    -

    fix drude/transform/inverse command -

    -

    Syntax: -

    -
    fix ID group-ID style keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • style = drude/transform/direct or drude/transform/inverse -
    -

    Examples: -

    -
    fix 3 all drude/transform/direct
-fix 1 all drude/transform/inverse 
-
    -

    Description: -

    -

    Transform the coordinates of Drude oscillators from real to reduced -and back for thermalizing the Drude oscillators as described in -(Lamoureux) using a Nose-Hoover thermostat. This fix is -designed to be used with the thermalized Drude oscillator -model. Polarizable models in LAMMPS are -described in this Section. -

    -

    Drude oscillators are a pair of atoms representing a single -polarizable atom. Ideally, the mass of Drude particles would vanish -and their positions would be determined self-consistently by iterative -minimization of the energy, the cores' positions being fixed. It is -however more efficient and it yields comparable results, if the Drude -oscillators (the motion of the Drude particle relative to the core) -are thermalized at a low temperature. In that case, the Drude -particles need a small mass. -

    -

    The thermostats act on the reduced degrees of freedom, which are -defined by the following equations. Note that in these equations -upper case denotes atomic or center of mass values and lower case -denotes Drude particle or dipole values. Primes denote the transformed -(reduced) values, while bare letters denote the original values. -

    -

    Masses: \begin{equation} M' = M + m \end{equation} -\begin{equation} m' = \frac {M\, m } {M'} \end{equation} -Positions: \begin{equation} X' = \frac {M\, X + m\, x} {M'} -\end{equation} \begin{equation} x' = x - X \end{equation} -Velocities: \begin{equation} V' = \frac {M\, V + m\, v} {M'} -\end{equation} \begin{equation} v' = v - V \end{equation} -Forces: \begin{equation} F' = F + f \end{equation} -\begin{equation} f' = \frac { M\, f - m\, F} {M'} -\end{equation} -

    -

    This transform conserves the total kinetic energy -\begin{equation} \frac 1 2 \, (M\, V^2\ + m\, v^2) -= \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) \end{equation} -and the virial defined with absolute positions -\begin{equation} X\, F + x\, f = X'\, F' + x'\, f' \end{equation} -

    -
    - -

    This fix requires each atom know whether it is a Drude particle or -not. You must therefore use the fix drude command to -specify the Drude status of each atom type. -

    -

    IMPORTANT NOTE: only the Drude core atoms need to be in the group -specified for this fix. A Drude electron will be transformed together -with its cores even if it is not itself in the group. It is safe to -include Drude electrons or non-polarizable atoms in the group. The -non-polarizable atoms will simply not be transformed. -

    -
    - -

    This fix does NOT perform time integration. It only transform masses, -coordinates, velocities and forces. Thus you must use separate time -integration fixes, like fix nve or fix -npt to actually update the velocities and positions of -atoms. In order to thermalize the reduced degrees of freedom at -different temperatures, two Nose-Hoover thermostats must be defined, -acting on two distinct groups. -

    -

    IMPORTANT NOTE: The fix drude/transform/direct command must appear -before any Nose-Hoover thermostating fixes. The fix -drude/transform/inverse command must appear after any Nose-Hoover -thermostating fixes. -

    -

    Example: -

    -
    fix fDIRECT all drude/transform/direct
-fix fNVT gCORES nvt temp 300.0 300.0 100.0
-fix fNVT gDRUDES nvt temp 1.0 1.0 100.0
-fix fINVERSE all drude/transform/inverse
-compute TDRUDE all temp/drude
-thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2] 
-
    -

    In this example, gCORES is the group of the atom cores and gDRUDES -is the group of the Drude particles (electrons). The centers of mass -of the Drude oscillators will be thermostated at 300.0 and the -internal degrees of freedom will be thermostated at 1.0. The -temperatures of cores and Drude particles, in center-of-mass and -relatice coordinates, are calculated using compute -temp/drude -

    -

    In addition, if you want to use a barostat to simulate a system at -constant pressure, only one of the Nose-Hoover fixes must be npt, -the other one should be nvt. You must add a compute temp/com and a -fix_modify command so that the temperature of the npt fix be just -that of its group but the pressure be the overall pressure -thermo_press. -

    -

    Example: -

    -
    compute cTEMP_CORE gCORES temp/com
-fix fDIRECT all drude/transform/direct
-fix fNPT gCORES npt temp 298.0 298.0 100.0 iso 1.0 1.0 500.0
-fix_modify fNPT temp cTEMP_CORE press thermo_press
-fix fNVT gDRUDES nvt temp 5.0 5.0 100.0
-fix fINVERSE all drude/transform/inverse 
-
    -

    In this example, gCORES is the group of the atom cores and gDRUDES -is the group of the Drude particles. The centers of mass of the Drude -oscillators will be thermostated at 298.0 and the internal degrees of -freedom will be thermostated at 5.0. The whole system will be -barostated at 1.0. -

    -

    In order to avoid the flying ice cube problem (irreversible transfer -of linear momentum to the center of mass of the system), you may need -to add a fix momentum command like such as -

    -
    fix fMOMENTUM all momentum 100 linear 1 1 1 
-
    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix drude, -fix langevin/drude, -compute temp/drude, -pair_style thole -

    -

    Default: none -

    -
    - - - -

    (Lamoureux) Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003). -

    - diff --git a/doc/doc2/fix_dt_reset.html b/doc/doc2/fix_dt_reset.html deleted file mode 100644 index 039327b172..0000000000 --- a/doc/doc2/fix_dt_reset.html +++ /dev/null @@ -1,96 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix dt/reset command -

    -

    Syntax: -

    -
    fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... 
-
    -
    • ID, group-ID are documented in fix command -
    • dt/reset = style name of this fix command -
    • N = recompute dt every N timesteps -
    • Tmin = minimum dt allowed which can be NULL (time units) -
    • Tmax = maximum dt allowed which can be NULL (time units) -
    • Xmax = maximum distance for an atom to move in one timestep (distance units) -
    • zero or more keyword/value pairs may be appended -
    • keyword = units -
    -
      units value = lattice or box
-    lattice = Xmax is defined in lattice units
-    box = Xmax is defined in simulation box units 
-
    -

    Examples: -

    -
    fix 5 all dt/reset 10 1.0e-5 0.01 0.1
-fix 5 all dt/reset 10 0.01 2.0 0.2 units box 
-
    -

    Description: -

    -

    Reset the timestep size every N steps during a run, so that no atom -moves further than Xmax, based on current atom velocities and forces. -This can be useful when starting from a configuration with overlapping -atoms, where forces will be large. Or it can be useful when running -an impact simulation where one or more high-energy atoms collide with -a solid, causing a damage cascade. -

    -

    This fix overrides the timestep size setting made by the -timestep command. The new timestep size dt is -computed in the following manner. -

    -

    For each atom, the timestep is computed that would cause it to -displace Xmax on the next integration step, as a function of its -current velocity and force. Since performing this calculation exactly -would require the solution to a quartic equation, a cheaper estimate -is generated. The estimate is conservative in that the atom's -displacement is guaranteed not to exceed Xmax, though it may be -smaller. -

    -

    Given this putative timestep for each atom, the minimum timestep value -across all atoms is computed. Then the Tmin and Tmax bounds are -applied, if specified. If one (or both) is specified as NULL, it is -not applied. -

    -

    When the run style is respa, this fix resets the -outer loop (largest) timestep, which is the same timestep that the -timestep command sets. -

    -

    Note that the cumulative simulation time (in time units), which -accounts for changes in the timestep size as a simulation proceeds, -can be accessed by the thermo_style time keyword. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar stores -the last timestep on which the timestep was reset to a new value. -

    -

    The scalar value calculated by this fix is "intensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    timestep -

    -

    Default: -

    -

    The option defaults is units = lattice. -

    - diff --git a/doc/doc2/fix_efield.html b/doc/doc2/fix_efield.html deleted file mode 100644 index 339e4db521..0000000000 --- a/doc/doc2/fix_efield.html +++ /dev/null @@ -1,170 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix efield command -

    -

    Syntax: -

    -
    fix ID group-ID efield ex ey ez keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • efield = style name of this fix command - -
    • ex,ey,ez = E-field component values (electric field units) - -
    • any of ex,ey,ez can be a variable (see below) - -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = region or energy - -
        region value = region-ID
-    region-ID = ID of region atoms must be in to have added force
-  energy value = v_name
-    v_name = variable with name that calculates the potential energy of each atom in the added E-field 
-
      - -
    -

    Examples: -

    -
    fix kick external-field efield 1.0 0.0 0.0
-fix kick external-field efield 0.0 0.0 v_oscillate 
-
    -

    Description: -

    -

    Add a force F = qE to each charged atom in the group due to an -external electric field being applied to the system. If the system -contains point-dipoles, also add a torque on the dipoles due to the -external electric field. -

    -

    For charges, any of the 3 quantities defining the E-field components -can be specified as an equal-style or atom-style -variable, namely ex, ey, ez. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the E-field component. -

    -

    For point-dipoles, equal-style variables can be used, but atom-style -variables are not currently supported, since they imply a spatial -gradient in the electric field which means additional terms with -gradients of the field are required for the force and torque on -dipoles. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent E-field. -

    -

    Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent E-field -with optional time-dependence as well. -

    -

    If the region keyword is used, the atom must also be in the -specified geometric region in order to have force added -to it. -

    -
    - -

    Adding a force or torque to atoms implies a change in their potential -energy as they move or rotate due to the applied E-field. -

    -

    For dynamics via the "run" command, this energy can be optionally -added to the system's potential energy for thermodynamic output (see -below). For energy minimization via the "minimize" command, this -energy must be added to the system's potential energy to formulate a -self-consistent minimization problem (see below). -

    -

    The energy keyword is not allowed if the added field is a constant -vector (ex,ey,ez), with all components defined as numeric constants -and not as variables. This is because LAMMPS can compute the energy -for each charged particle directly as E = -x dot qE = -q (x*ex + y*ey -+ z*ez), so that -Grad(E) = F. Similarly for point-dipole particles -the energy can be computed as E = -mu dot E = -(mux*ex + muy*ey + -muz*ez). -

    -

    The energy keyword is optional if the added force is defined with -one or more variables, and if you are performing dynamics via the -run command. If the keyword is not used, LAMMPS will set -the energy to 0.0, which is typically fine for dynamics. -

    -

    The energy keyword is required if the added force is defined with -one or more variables, and you are performing energy minimization via -the "minimize" command for charged particles. It is not required for -point-dipoles, but a warning is issued since the minimizer in LAMMPS -does not rotate dipoles, so you should not expect to be able to -minimize the orientation of dipoles in an applied electric field. -

    -

    The energy keyword specifies the name of an atom-style -variable which is used to compute the energy of each -atom as function of its position. Like variables used for ex, ey, -ez, the energy variable is specified as v_name, where name is the -variable name. -

    -

    Note that when the energy keyword is used during an energy -minimization, you must insure that the formula defined for the -atom-style variable is consistent with the force -variable formulas, i.e. that -Grad(E) = F. For example, if the force -due to the electric field were a spring-like F = kx, then the energy -formula should be E = -0.5kx^2. If you don't do this correctly, the -minimization will not converge properly. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the potential "energy" inferred by the added force due to -the electric field to the system's potential energy as part of -thermodynamic output. This is a fictitious -quantity but is needed so that the minimize command -can include the forces added by this fix in a consistent manner. -I.e. there is a decrease in potential energy when atoms move in the -direction of the added force due to the electric field. -

    -

    This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various output -commands. The scalar is the potential -energy discussed above. The vector is the total force added to the -group of atoms. The scalar and vector values calculated by this fix -are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. -

    -

    IMPORTANT NOTE: If you want the fictitious potential energy associated -with the added forces to be included in the total potential energy of -the system (the quantity being minimized), you MUST enable the -fix_modify energy option for this fix. -

    -

    Restrictions: -

    -

    This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix addforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_enforce2d.html b/doc/doc2/fix_enforce2d.html deleted file mode 100644 index 87b0546b43..0000000000 --- a/doc/doc2/fix_enforce2d.html +++ /dev/null @@ -1,74 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix enforce2d command -

    -

    fix enforce2d/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID enforce2d 
-
    -
    • ID, group-ID are documented in fix command -
    • enforce2d = style name of this fix command -
    -

    Examples: -

    -
    fix 5 all enforce2d 
-
    -

    Description: -

    -

    Zero out the z-dimension velocity and force on each atom in the group. -This is useful when running a 2d simulation to insure that atoms do -not move from their initial z coordinate. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_evaporate.html b/doc/doc2/fix_evaporate.html deleted file mode 100644 index 5918faffc4..0000000000 --- a/doc/doc2/fix_evaporate.html +++ /dev/null @@ -1,109 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix evaporate command -

    -

    Syntax: -

    -
    fix ID group-ID evaporate N M region-ID seed 
-
    -
    • ID, group-ID are documented in fix command - -
    • evaporate = style name of this fix command - -
    • N = delete atoms every this many timesteps - -
    • M = number of atoms to delete each time - -
    • region-ID = ID of region within which to perform deletions - -
    • seed = random number seed to use for choosing atoms to delete - -
    • zero or more keyword/value pairs may be appended - -
      keyword = molecule
-  molecule value = no or yes 
-
      - -
    -

    Examples: -

    -
    fix 1 solvent evaporate 1000 10 surface 49892
-fix 1 solvent evaporate 1000 10 surface 38277 molecule yes 
-
    -

    Description: -

    -

    Remove M atoms from the simulation every N steps. This can be used, -for example, to model evaporation of solvent particles or moleclues -(i.e. drying) of a system. Every N steps, the number of atoms in the -fix group and within the specifed region are counted. M of these are -chosen at random and deleted. If there are less than M eligible -particles, then all of them are deleted. -

    -

    If the setting for the molecule keyword is no, then only single -atoms are deleted. In this case, you should insure you do not delete -only a portion of a molecule (only some of its atoms), or LAMMPS will -soon generate an error when it tries to find those atoms. LAMMPS will -warn you if any of the atoms eligible for deletion have a non-zero -molecule ID, but does not check for this at the time of deletion. -

    -

    If the setting for the molecule keyword is yes, then when an atom -is chosen for deletion, the entire molecule it is part of is deleted. -The count of deleted atoms is incremented by the number of atoms in -the molecule, which may make it exceed M. If the molecule ID of the -chosen atom is 0, then it is assumed to not be part of a molecule, and -just the single atom is deleted. -

    -

    As an example, if you wish to delete 10 water molecules every N -steps, you should set M to 30. If only the water's oxygen atoms -were in the fix group, then two hydrogen atoms would be deleted when -an oxygen atom is selected for deletion, whether the hydrogens are -inside the evaporation region or not. -

    -

    Note that neighbor lists are re-built on timesteps that atoms are -removed. Thus you should not remove atoms too frequently or you will -incur overhead due to the cost of building neighbor lists. -

    -

    IMPORTANT NOTE: If you are monitoring the temperature of a system -where the atom count is changing due to evaporation, you typically -should use the compute_modify dynamic yes -command for the temperature compute you are using. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar, which can be accessed by various -output commands. The scalar is the -cummulative number of deleted atoms. The scalar value calculated by -this fix is "intensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix deposit -

    -

    Default: -

    -

    The option defaults are molecule = no. -

    - diff --git a/doc/doc2/fix_external.html b/doc/doc2/fix_external.html deleted file mode 100644 index 717bc456e4..0000000000 --- a/doc/doc2/fix_external.html +++ /dev/null @@ -1,163 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix external command -

    -

    Syntax: -

    -
    fix ID group-ID external mode args 
-
    -
    • ID, group-ID are documented in fix command - -
    • external = style name of this fix command - -
    • mode = pf/callback or pf/array - -
        pf/callback args = Ncall Napply
-    Ncall = make callback every Ncall steps
-    Napply = apply callback forces every Napply steps
-  pf/array args = Napply
-    Napply = apply array forces every Napply steps 
-
      - -
    -

    Examples: -

    -
    fix 1 all external pf/callback 1 1
-fix 1 all external pf/callback 100 1
-fix 1 all external pf/array 10 
-
    -

    Description: -

    -

    This fix allows external programs that are running LAMMPS through its -library interface to modify certain -LAMMPS properties on specific timesteps, similar to the way other -fixes do. The external driver can be a C/C++ or Fortran -program or a Python -script. -

    -
    - -

    If mode is pf/callback then the fix will make a callback every -Ncall timesteps or minimization iterations to the external program. -The external program computes forces on atoms by setting values in an -array owned by the fix. The fix then adds these forces to each atom -in the group, once every Napply steps, similar to the way the fix -addforce command works. Note that if Ncall > -Napply, the force values produced by one callback will persist, and -be used multiple times to update atom forces. -

    -

    The callback function "foo" is invoked by the fix as: -

    -
    foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal); 
-
    -

    The arguments are as follows: -

    -
    • ptr = pointer provided by and simply passed back to external driver -
    • timestep = current LAMMPS timestep -
    • nlocal = # of atoms on this processor -
    • ids = list of atom IDs on this processor -
    • x = coordinates of atoms on this processor -
    • fexternal = forces to add to atoms on this processor -
    -

    Note that timestep is a "bigint" which is defined in src/lmptype.h, -typically as a 64-bit integer. -

    -

    Fexternal are the forces returned by the driver program. -

    -

    The fix has a set_callback() method which the external driver can call -to pass a pointer to its foo() function. See the -couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an -example of how this is done. This sample application performs -classical MD using quantum forces computed by a density functional -code Quest. -

    - - -
    - -

    If mode is pf/array then the fix simply stores force values in an -array. The fix adds these forces to each atom in the group, once -every Napply steps, similar to the way the fix -addforce command works. -

    -

    The name of the public force array provided by the FixExternal -class is -

    -
    double **fexternal; 
-
    -

    It is allocated by the FixExternal class as an (N,3) array where N is -the number of atoms owned by a processor. The 3 corresponds to the -fx, fy, fz components of force. -

    -

    It is up to the external program to set the values in this array to -the desired quantities, as often as desired. For example, the driver -program might perform an MD run in stages of 1000 timesteps each. In -between calls to the LAMMPS run command, it could retrieve -atom coordinates from LAMMPS, compute forces, set values in fexternal, -etc. -

    -
    - -

    To use this fix during energy minimization, the energy corresponding -to the added forces must also be set so as to be consistent with the -added forces. Otherwise the minimization will not converge correctly. -

    -

    This can be done from the external driver by calling this public -method of the FixExternal class: -

    -
    void set_energy(double eng); 
-
    -

    where eng is the potential energy. Eng is an extensive quantity, -meaning it should be the sum over per-atom energies of all affected -atoms. It should also be provided in energy units -consistent with the simulation. See the details below for how to -insure this energy setting is used appropriately in a minimization. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the potential "energy" set by the external driver to the -system's potential energy as part of thermodynamic -output. This is a fictitious quantity but is -needed so that the minimize command can include the -forces added by this fix in a consistent manner. I.e. there is a -decrease in potential energy when atoms move in the direction of the -added force. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -potential energy discussed above. The scalar stored by this fix -is "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    IMPORTANT NOTE: If you want the fictitious potential energy associated -with the added forces to be included in the total potential energy of -the system (the quantity being minimized), you MUST enable the -fix_modify energy option for this fix. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_freeze.html b/doc/doc2/fix_freeze.html deleted file mode 100644 index ec829e4102..0000000000 --- a/doc/doc2/fix_freeze.html +++ /dev/null @@ -1,93 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix freeze command -

    -

    fix freeze/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID freeze 
-
    -
    • ID, group-ID are documented in fix command -
    • freeze = style name of this fix command -
    -

    Examples: -

    -
    fix 2 bottom freeze 
-
    -

    Description: -

    -

    Zero out the force and torque on a granular particle. This is useful -for preventing certain particles from moving in a simulation. The -granular pair styles also detect if this fix has been -defined and compute interactions between frozen and non-frozen -particles appropriately, as if the frozen particle has infinite mass. -A similar functionality for normal (point) particles can be obtained -using fix setforce. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global 3-vector of forces, which can be accessed -by various output commands. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    There can only be a single freeze fix defined. This is because other -the granular pair styles treat frozen particles -differently and need to be able to reference a single group to which -this fix is applied. -

    -

    Related commands: -

    -

    atom_style sphere, fix setforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_gcmc.html b/doc/doc2/fix_gcmc.html deleted file mode 100644 index 21864923c1..0000000000 --- a/doc/doc2/fix_gcmc.html +++ /dev/null @@ -1,369 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix gcmc command -

    -

    Syntax: -

    -
    fix ID group-ID gcmc N X M type seed T mu displace keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • gcmc = style name of this fix command - -
    • N = invoke this fix every N steps - -
    • X = average number of GCMC exchanges to attempt every N steps - -
    • M = average number of MC moves to attempt every N steps - -
    • type = atom type for inserted atoms (must be 0 if mol keyword used) - -
    • seed = random # seed (positive integer) - -
    • T = temperature of the ideal gas reservoir (temperature units) - -
    • mu = chemical potential of the ideal gas reservoir (energy units) - -
    • translate = maximum Monte Carlo translation distance (length units) - -
    • zero or more keyword/value pairs may be appended to args - -
      keyword = mol, region, maxangle, pressure, fugacity_coeff, full_energy, charge, group, grouptype, intra_energy, or tfac_insert
-  mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
-  shake value = fix-ID
-    fix-ID = ID of fix shake command
-  region value = region-ID
-    region-ID = ID of region where MC moves are allowed 
-  maxangle value = maximum molecular rotation angle (degrees) 
-  pressure value = pressure of the gas reservoir (pressure units)
-  fugacity_coeff value = fugacity coefficient of the gas reservoir (unitless) 
-  full_energy = compute the entire system energy when performing MC moves
-  charge value = charge of inserted atoms (charge units)
-  group value = group-ID
-    group-ID = group-ID for inserted atoms (string)
-  grouptype values = type group-ID 
-    type = atom type (int)
-    group-ID = group-ID for inserted atoms (string)
-  intra_energy value = intramolecular energy (energy units)
-  tfac_insert value = scale up/down temperature of inserted atoms (unitless) 
-
      - -
    -

    Examples: -

    -
    fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
-fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
-fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk 
-
    -

    Description: -

    -

    This fix performs grand canonical Monte Carlo (GCMC) exchanges of -atoms or molecules of the given type with an imaginary ideal gas reservoir at -the specified T and chemical potential (mu) as discussed in -(Frenkel). If used with the fix nvt command, -simulations in the grand canonical ensemble (muVT, constant chemical -potential, constant volume, and constant temperature) can be -performed. Specific uses include computing isotherms in microporous -materials, or computing vapor-liquid coexistence curves. -

    -

    Every N timesteps the fix attempts a number of GCMC exchanges (insertions -or deletions) of gas atoms or molecules of -the given type between the simulation cell and the imaginary -reservoir. It also attempts a number of Monte Carlo -moves (translations and molecule rotations) of gas of the given type -within the simulation cell or region. The average number of -attempted GCMC exchanges is X. The average number of attempted MC moves is M. -M should typically be chosen to be -approximately equal to the expected number of gas atoms or molecules -of the given type within the simulation cell or region, -which will result in roughly one -MC translation per atom or molecule per MC cycle. -

    -

    For MC moves of molecular gasses, rotations and translations are each -attempted with 50% probability. For MC moves of atomic gasses, -translations are attempted 100% of the time. For MC exchanges of -either molecular or atomic gasses, deletions and insertions are each -attempted with 50% probability. -

    -

    All inserted particles are always assigned to two groups: the default group -"all" and the group specified in the fix gcmc command (which can also -be "all"). In addition, particles are also added to any groups specified -by the group and grouptype keywords. -If inserted particles are individual atoms, they are -assigned the atom type given by the type argument. If they are molecules, -the type argument has no effect and must be set to zero. Instead, -the type of each atom in the inserted molecule is specified -in the file read by the molecule command. -

    -

    This fix cannot be used to perform MC insertions of gas atoms or -molecules other than the exchanged type, but MC deletions, -translations, and rotations can be performed on any atom/molecule in -the fix group. All atoms in the simulation cell can be moved using -regular time integration translations, e.g. via -fix_nvt, resulting in a hybrid GCMC+MD simulation. A -smaller-than-usual timestep size may be needed when running such a -hybrid simulation, especially if the inserted molecules are not well -equilibrated. -

    -

    This command may optionally use the region keyword to define an -exchange and move volume. The specified region must have been -previously defined with a region command. It must be -defined with side = in. Insertion attempts occur only within the -specified region. For non-rectangular regions, random trial -points are generated within the rectangular bounding box until a point is found -that lies inside the region. If no valid point is generated after 1000 trials, -no insertion is performed, but it is counted as an attempted insertion. -Move and deletion attempt candidates are selected -from gas atoms or molecules within the region. If there are no candidates, -no move or deletion is performed, but it is counted as an attempt move -or deletion. If an attempted move places the atom or molecule center-of-mass outside -the specified region, a new attempted move is generated. This process is repeated -until the atom or molecule center-of-mass is inside the specified region. -

    -

    If used with fix_nvt, the temperature of the imaginary -reservoir, T, should be set to be equivalent to the target temperature -used in fix_nvt. Otherwise, the imaginary reservoir -will not be in thermal equilibrium with the simulation cell. Also, -it is important that the temperature used by fix nvt be dynamic, -which can be achieved as follows: -

    -
    compute mdtemp mdatoms temp 
-compute_modify mdtemp dynamic yes
-fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
-fix_modify mdnvt temp mdtemp 
-
    -

    Note that neighbor lists are re-built every timestep that this fix is -invoked, so you should not set N to be too small. However, periodic -rebuilds are necessary in order to avoid dangerous rebuilds and missed -interactions. Specifically, avoid performing so many MC translations -per timestep that atoms can move beyond the neighbor list skin -distance. See the neighbor command for details. -

    -

    When an atom or molecule is to be inserted, its -coordinates are chosen at a random position within the current -simulation cell or region, and new atom velocities are randomly chosen from -the specified temperature distribution given by T. The effective -temperature for new atom velocities can be increased or decreased -using the optional keyword tfac_insert (see below). Relative -coordinates for atoms in a molecule are taken from the template -molecule provided by the user. The center of mass of the molecule -is placed at the insertion point. The orientation of the molecule -is chosen at random by rotating about this point. -

    -

    Individual atoms are inserted, unless the mol keyword is used. It -specifies a template-ID previously defined using the -molecule command, which reads a file that defines the -molecule. The coordinates, atom types, charges, etc, as well as any -bond/angle/etc and special neighbor information for the molecule can -be specified in the molecule file. See the molecule -command for details. The only settings required to be in this file -are the coordinates and types of atoms in the molecule. -

    -

    When not using the mol keyword, you should ensure you do not delete -atoms that are bonded to other atoms, or LAMMPS will -soon generate an error when it tries to find bonded neighbors. LAMMPS will -warn you if any of the atoms eligible for deletion have a non-zero -molecule ID, but does not check for this at the time of deletion. -

    -

    If you wish to insert molecules via the mol keyword, that will have -their bonds or angles constrained via SHAKE, use the shake keyword, -specifying as its value the ID of a separate fix -shake command which also appears in your input script. -

    -

    Optionally, users may specify the maximum rotation angle for -molecular rotations using the maxangle keyword and specifying -the angle in degrees. Rotations are performed by generating a random -point on the unit sphere and a random rotation angle on the -range [0,maxangle). The molecule is then rotated by that angle about an -axis passing through the molecule center of mass. The axis is parallel -to the unit vector defined by the point on the unit sphere. -The same procedure is used for randomly rotating molecules when they -are inserted, except that the maximum angle is 360 degrees. -

    -

    Note that fix GCMC does not use configurational bias -MC or any other kind of sampling of intramolecular degrees of freedom. -Inserted molecules can have different orientations, but they will all -have the same intramolecular configuration, -which was specified in the molecule command input. -

    -

    For atomic gasses, inserted atoms have the specified atom type, but -deleted atoms are any atoms that have been inserted or that belong -to the user-specified fix group. For molecular gasses, exchanged -molecules use the same atom types as in the template molecule -supplied by the user. In both cases, exchanged -atoms/molecules are assigned to two groups: the default group "all" -and the group specified in the fix gcmc command (which can also be -"all"). -

    -

    The gas reservoir pressure can be specified using the pressure -keyword, in which case the user-specified chemical potential is -ignored. For non-ideal gas reservoirs, the user may also specify the -fugacity coefficient using the fugacity_coeff keyword. -

    -

    The full_energy option means that fix GCMC will compute the total -potential energy of the entire simulated system. The total system -energy before and after the proposed GCMC move is then used in the -Metropolis criterion to determine whether or not to accept the -proposed GCMC move. By default, this option is off, in which case -only partial energies are computed to determine the difference in -energy that would be caused by the proposed GCMC move. -

    -

    The full_energy option is needed for systems with complicated -potential energy calculations, including the following: -

    -
    • long-range electrostatics (kspace) -
    • many-body pair styles -
    • hybrid pair styles -
    • eam pair styles -
    • triclinic systems -
    • need to include potential energy contributions from other fixes -
    -

    In these cases, LAMMPS will automatically apply the full_energy -keyword and issue a warning message. -

    -

    When the mol keyword is used, the full_energy option also includes -the intramolecular energy of inserted and deleted molecules. If this -is not desired, the intra_energy keyword can be used to define an -amount of energy that is subtracted from the final energy when a molecule -is inserted, and added to the initial energy when a molecule is -deleted. For molecules that have a non-zero intramolecular energy, this -will ensure roughly the same behavior whether or not the full_energy -option is used. -

    -

    Inserted atoms and molecules are assigned random velocities based on the -specified temperature T. Because the relative velocity of -all atoms in the molecule is zero, this may result in inserted molecules -that are systematically too cold. In addition, the intramolecular potential -energy of the inserted molecule may cause the kinetic energy -of the molecule to quickly increase or decrease after insertion. -The tfac_insert keyword allows the user to counteract these effects -by changing the temperature used to assign velocities to -inserted atoms and molecules by a constant factor. For a -particular application, some experimentation may be required -to find a value of tfac_insert that results in inserted molecules that -equilibrate quickly to the correct temperature. -

    -

    Some fixes have an associated potential energy. Examples of such fixes -include: efield, gravity, -addforce, langevin, -restrain, temp/berendsen, -temp/rescale, and wall fixes. -For that energy to be included in the total potential energy of the -system (the quantity used when performing GCMC moves), -you MUST enable the fix_modify energy option for -that fix. The doc pages for individual fix commands -specify if this should be done. -

    -

    Use the charge option to insert atoms with a user-specified point -charge. Note that doing so will cause the system to become non-neutral. -LAMMPS issues a warning when using long-range electrostatics (kspace) -with non-neutral systems. See the -compute_group_group documentation for more -details about simulating non-neutral systems with kspace on. -

    -

    Use of this fix typically will cause the number of atoms to fluctuate, -therefore, you will want to use the -compute_modify command to insure that the -current number of atoms is used as a normalizing factor each time -temperature is computed. Here is the necessary command: -

    -
    compute_modify thermo_temp dynamic yes 
-
    -

    If LJ units are used, note that a value of 0.18292026 is used by this -fix as the reduced value for Planck's constant. This value was -derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 * -epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and -mass = 39.948 amu. -

    -

    The group keyword assigns all inserted atoms to the group -of the group-ID value. The grouptype keyword assigns all -inserted atoms of the specified type to the group -of the group-ID value. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the fix to binary restart -files. This includes information about the random -number generator seed, the next timestep for MC exchanges, etc. See -the read_restart command for info on how to -re-specify a fix in an input script that reads a restart file, so that -the operation of the fix continues in an uninterrupted fashion. -

    -

    None of the fix_modify options are relevant to this -fix. -

    -

    This fix computes a global vector of length 8, which can be accessed -by various output commands. The vector -values are the following global cumulative quantities: -

    -
    • 1 = translation attempts -
    • 2 = translation successes -
    • 3 = insertion attempts -
    • 4 = insertion successes -
    • 5 = deletion attempts -
    • 6 = deletion successes -
    • 7 = rotation attempts -
    • 8 = rotation successes -
    -

    The vector values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    Do not set "neigh_modify once yes" or else this fix will never be -called. Reneighboring is required. -

    -

    Can be run in parallel, but aspects of the GCMC part will not scale -well in parallel. Only usable for 3D simulations. -

    -

    Note that very lengthy simulations involving insertions/deletions of -billions of gas molecules may run out of atom or molecule IDs and -trigger an error, so it is better to run multiple shorter-duration -simulations. Likewise, very large molecules have not been tested -and may turn out to be problematic. -

    -

    Use of multiple fix gcmc commands in the same input script can be -problematic if using a template molecule. The issue is that the -user-referenced template molecule in the second fix gcmc command -may no longer exist since it might have been deleted by the first -fix gcmc command. An existing template molecule will need to be -referenced by the user for each subsequent fix gcmc command. -

    -

    Related commands: -

    -

    fix atom/swap, -fix nvt, neighbor, -fix deposit, fix evaporate, -delete_atoms -

    -

    Default: -

    -

    The option defaults are mol = no, maxangle = 10, full_energy = no, -except for the situations where full_energy is required, as -listed above. -

    -
    - - - -

    (Frenkel) Frenkel and Smit, Understanding Molecular Simulation, -Academic Press, London, 2002. -

    - diff --git a/doc/doc2/fix_gld.html b/doc/doc2/fix_gld.html deleted file mode 100644 index 840a47265b..0000000000 --- a/doc/doc2/fix_gld.html +++ /dev/null @@ -1,171 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix gld command -

    -

    Syntax: -

    -
    fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • gld = style name of this fix command - -
    • Tstart,Tstop = desired temperature at start/end of run (temperature units) - -
    • N_k = number of terms in the Prony series representation of the memory kernel - -
    • seed = random number seed to use for white noise (positive integer) - -
    • series = pprony is presently the only available option - -
    • c_k = the weight of the kth term in the Prony series (mass per time units) - -
    • tau_k = the time constant of the kth term in the Prony series (time units) - -
    • zero or more keyword/value pairs may be appended - -
      keyword = frozen or zero
-  frozen value = no or yes
-    no = initialize extended variables using values drawn from equilibrium distribution at Tstart
-    yes = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
-  zero value = no or yes
-    no = do not set total random force to zero
-    yes = set total random force to zero 
-
      - -
    -

    Examples: -

    -
    fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes
-fix 3 rouse gld 7.355 7.355 4 48823 pprony 107.1 0.02415 186.0 0.04294 428.6 0.09661 1714 0.38643 
-
    -

    Description: -

    -

    Applies Generalized Langevin Dynamics to a group of atoms, as -described in (Baczewski). This is intended to model the -effect of an implicit solvent with a temporally non-local dissipative -force and a colored Gaussian random force, consistent with the -Fluctuation-Dissipation Theorem. The functional form of the memory -kernel associated with the temporally non-local force is constrained -to be a Prony series. -

    -

    IMPORTANT NOTE: While this fix bears many similarities to fix -langevin, it has one significant -difference. Namely, fix gld performs time integration, -whereas fix langevin does NOT. To this end, the -specification of another fix to perform time integration, such as fix -nve, is NOT necessary. -

    -

    With this fix active, the force on the jth atom is given as -

    -
    -
    -

    Here, the first term is representative of all conservative (pairwise, -bonded, etc) forces external to this fix, the second is the temporally -non-local dissipative force given as a Prony series, and the third is -the colored Gaussian random force. -

    -

    The Prony series form of the memory kernel is chosen to enable an -extended variable formalism, with a number of exemplary mathematical -features discussed in (Baczewski). In particular, 3N_k -extended variables are added to each atom, which effect the action of -the memory kernel without having to explicitly evaluate the integral -over time in the second term of the force. This also has the benefit -of requiring the generation of uncorrelated random forces, rather than -correlated random forces as specified in the third term of the force. -

    -

    Presently, the Prony series coefficients are limited to being greater -than or equal to zero, and the time constants are limited to being -greater than zero. To this end, the value of series MUST be set to -pprony, for now. Future updates will allow for negative coefficients -and other representations of the memory kernel. It is with these -updates in mind that the series option was included. -

    -

    The units of the Prony series coefficients are chosen to be mass per -time to ensure that the numerical integration scheme stably approaches -the Newtonian and Langevin limits. Details of these limits, and the -associated numerical concerns are discussed in -(Baczewski). -

    -

    The desired temperature at each timestep is ramped from Tstart to -Tstop over the course of the next run. -

    -

    The random # seed must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random -numbers. Thus the dynamics of the system will not be identical on two -runs on different numbers of processors. -

    -
    - -

    The keyword/value option pairs are used in the following ways. -

    -

    The keyword frozen can be used to specify how the extended variables -associated with the GLD memory kernel are initialized. Specifying no -(the default), the initial values are drawn at random from an -equilibrium distribution at Tstart, consistent with the -Fluctuation-Dissipation Theorem. Specifying yes, initializes the -extended variables to zero. -

    -

    The keyword zero can be used to eliminate drift due to the -thermostat. Because the random forces on different atoms are -independent, they do not sum exactly to zero. As a result, this fix -applies a small random force to the entire system, and the -center-of-mass of the system undergoes a slow random walk. If the -keyword zero is set to yes, the total random force is set exactly -to zero by subtracting off an equal part of it from each atom in the -group. As a result, the center-of-mass of a system with zero initial -momentum will not drift over time. -

    -
    - -

    Restart, run start/stop, minimize info: -

    -

    The instantaneous values of the extended variables are written to -binary restart files. Because the state of the random -number generator is not saved in restart files, this means you cannot -do "exact" restarts with this fix, where the simulation continues on -the same as if no restart had taken place. However, in a statistical -sense, a restarted simulation should produce the same behavior. -

    -

    None of the fix_modify options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various output commands. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix langevin, fix viscous, -pair_style dpd/tstat -

    -

    Default: -

    -

    The option defaults are frozen = no, zero = no. -

    -
    - - - -

    (Baczewski) A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013). -

    - diff --git a/doc/doc2/fix_gle.html b/doc/doc2/fix_gle.html deleted file mode 100644 index ec749d513b..0000000000 --- a/doc/doc2/fix_gle.html +++ /dev/null @@ -1,170 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix gle command -

    -

    Syntax: -

    -
    fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride] 
-
    -
    • ID, group-ID are documented in fix command - -
    • gle = style name of this fix command - -
    • Ns = number of additional fictitious momenta - -
    • Tstart, Tstop = temperature ramp during the run - -
    • Amatrix = file to read the drift matrix A from - -
    • seed = random number seed to use for generating noise (positive integer) - -
    • zero or more keyword/value pairs may be appended - -keyword = noneq and/or every - noneq Cmatrix = file to read the non-equilibrium covariance matrix from - every stride = apply the GLE once every time steps. Reduces the accuracy - of the integration of the GLE, but has *no effect* on the accuracy of equilibrium - sampling. It might change sampling properties when used together with noneq. - -
    -

    Examples: -

    -

    fix 3 boundary gle 6 300 300 31415 smart.A -fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C -

    -

    Description: -

    -

    Apply a Generalized Langevin Equation (GLE) thermostat as described -in (Ceriotti). The formalism allows one to obtain a number -of different effects ranging from efficient sampling of all -vibrational modes in the system to inexpensive (approximate) -modelling of nuclear quantum effects. Contrary to -fix langevin, this fix performs both -thermostatting and evolution of the Hamiltonian equations of motion, so it -should not be used together with fix nve -- at least not -on the same atom groups. -

    -

    Each degree of freedom in the thermostatted group is supplemented -with Ns additional degrees of freedom s, and the equations of motion -become -

    -

    dq/dt=p/m -d(p,s)/dt=(F,0) - A(p,s) + B dW/dt -

    -

    where F is the physical force, A is the drift matrix (that generalizes -the friction in Langevin dynamics), B is the diffusion term and dW/dt -un-correlated Gaussian random forces. The A matrix couples the physical -(q,p) dynamics with that of the additional degrees of freedom, -and makes it possible to obtain effectively a history-dependent -noise and friction kernel. -

    -

    The drift matrix should be given as an external file Afile, -as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are -optimal for a given application and the system of choice can be -obtained from (GLE4MD). -

    -

    Equilibrium sampling a temperature T is obtained by specifiying the -target value as the Tstart and Tstop arguments, so that the diffusion -matrix that gives canonical sampling for a given A is computed automatically. -However, the GLE framework also allow for non-equilibrium sampling, that -can be used for instance to model inexpensively zero-point energy -effects (Ceriotti2). This is achieved specifying the -noneq keyword followed by the name of the file that contains the -static covariance matrix for the non-equilibrium dynamics. -

    -

    Since integrating GLE dynamics can be costly when used together with -simple potentials, one can use the every optional keyword to -apply the Langevin terms only once every several MD steps, in a -multiple time-step fashion. This should be used with care when doing -non-equilibrium sampling, but should have no effect on equilibrium -averages when using canonical sampling. -

    -

    The random number seed must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random numbers. -Thus the dynamics of the system will not be identical on two runs on -different numbers of processors. -

    -

    Note also that the Generalized Langevin Dynamics scheme that is -implemented by the fix gld scheme is closely related -to the present one. In fact, it should be always possible to cast the -Prony series form of the memory kernel used by GLD into an appropriate -input matrix for fix_gle. While the GLE scheme is more -general, the form used by fix gld can be more directly -related to the representation of an implicit solvent environment. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    The instantaneous values of the extended variables are written to -binary restart files. Because the state of the random -number generator is not saved in restart files, this means you cannot -do "exact" restarts with this fix, where the simulation continues on -the same as if no restart had taken place. However, in a statistical -sense, a restarted simulation should produce the same behavior. -Note however that you should use a different seed each time you -restart, otherwise the same sequence of random numbers will be used -each time, which might lead to stochastic synchronization and -subtle artefacts in the sampling. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Langevin thermostatting to the -system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". -

    -

    Restrictions: -

    -

    The GLE thermostat in its current implementation should not be used -with rigid bodies, SHAKE or RATTLE. It is expected that all the -thermostatted degrees of freedom are fully flexible, and the sampled -ensemble will not be correct otherwise. -

    -

    In order to perform constant-pressure simulations please use -fix press/berendsen, rather than -fix_npt, to avoid duplicate integration of the -equations of motion. -

    -

    This fix is part of the USER-MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix nvt, fix temp/rescale, fix -viscous, fix nvt, pair_style -dpd/tstat, fix_gld -

    -
    - - - -

    (Ceriotti) Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, -1170-80 (2010) -

    - - -

    (GLE4MD) http://epfl-cosmo.github.io/gle4md/ -

    - - -

    (Ceriotti2) Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, -030603 (2009) -

    - diff --git a/doc/doc2/fix_gravity.html b/doc/doc2/fix_gravity.html deleted file mode 100644 index cde892dc2a..0000000000 --- a/doc/doc2/fix_gravity.html +++ /dev/null @@ -1,154 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix gravity command -

    -

    fix gravity/cuda command -

    -

    fix gravity/omp command -

    -

    Syntax: -

    -
    fix ID group gravity magnitude style args 
-
    -
    • ID, group are documented in fix command - -
    • gravity = style name of this fix command - -
    • magnitude = size of acceleration (force/mass units) - -
    • magnitude can be a variable (see below) - -
    • style = chute or spherical or gradient or vector - -
        chute args = angle
-    angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
-    angle can be a variable (see below)
-  spherical args = phi theta
-    phi = azimuthal angle from +x axis (in degrees)
-    theta = angle from +z or +y axis in 3d/2d (in degrees)
-    phi or theta can be a variable (see below)
-  vector args = x y z
-    x y z = vector direction to apply the acceleration
-    x or y or z can be a variable (see below) 
-
      - -
    -

    Examples: -

    -
    fix 1 all gravity 1.0 chute 24.0
-fix 1 all gravity v_increase chute 24.0
-fix 1 all gravity 1.0 spherical 0.0 -180.0
-fix 1 all gravity 10.0 spherical v_phi v_theta
-fix 1 all gravity 100.0 vector 1 1 0 
-
    -

    Description: -

    -

    Impose an additional acceleration on each particle in the group. This -fix is typically used with granular systems to include a "gravity" -term acting on the macroscopic particles. More generally, it can -represent any kind of driving field, e.g. a pressure gradient inducing -a Poiseuille flow in a fluid. Note that this fix operates differently -than the fix addforce command. The addforce fix -adds the same force to each atom, independent of its mass. This -command imparts the same acceleration to each atom (force/mass). -

    -

    The magnitude of the acceleration is specified in force/mass units. -For granular systems (LJ units) this is typically 1.0. See the -units command for details. -

    -

    Style chute is typically used for simulations of chute flow where -the specified angle is the chute angle, with flow occurring in the +x -direction. For 3d systems, the tilt is away from the z axis; for 2d -systems, the tilt is away from the y axis. -

    -

    Style spherical allows an arbitrary 3d direction to be specified for -the acceleration vector. Phi and theta are defined in the usual -spherical coordinates. Thus for acceleration acting in the -z -direction, theta would be 180.0 (or -180.0). Theta = 90.0 and -phi = -90.0 would mean acceleration acts in the -y direction. For -2d systems, phi is ignored and theta is an angle in the xy plane -where theta = 0.0 is the y-axis. -

    -

    Style vector imposes an acceleration in the vector direction given -by (x,y,z). Only the direction of the vector is important; it's -length is ignored. For 2d systems, the z component is ignored. -

    -

    Any of the quantities magnitude, angle, phi, theta, x, y, -z which define the gravitational magnitude and direction, can be -specified as an equal-style variable. If the value is -a variable, it should be specified as v_name, where name is the -variable name. In this case, the variable will be evaluated each -timestep, and its value used to determine the quantity. You should -insure that the variable calculates a result in the approriate units, -e.g. force/mass or degrees. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent gravitational -field. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the gravitational potential energy of the system to the -system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. This scalar is the -gravitational potential energy of the particles in the defined field, -namely mass * (g dot x) for each particles, where x and mass are the -particles position and mass, and g is the gravitational field. The -scalar value calculated by this fix is "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    atom_style sphere, fix addforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_heat.html b/doc/doc2/fix_heat.html deleted file mode 100644 index b519acab60..0000000000 --- a/doc/doc2/fix_heat.html +++ /dev/null @@ -1,137 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix heat command -

    -

    Syntax: -

    -
    fix ID group-ID heat N eflux 
-
    -
    • ID, group-ID are documented in fix command - -
    • heat = style name of this fix command - -
    • N = add/subtract heat every this many timesteps - -
    • eflux = rate of heat addition or subtraction (energy/time units) - -
    • eflux can be a variable (see below) - -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = region - -
        region value = region-ID
-    region-ID = ID of region atoms must be in to have added force 
-
      - -
    -

    Examples: -

    -
    fix 3 qin heat 1 1.0
-fix 3 qin heat 10 v_flux
-fix 4 qout heat 1 -1.0 region top 
-
    -

    Description: -

    -

    Add non-translational kinetic energy (heat) to a group of atoms in a -manner that conserves their aggregate momentum. Two of these fixes -can be used to establish a temperature gradient across a simulation -domain by adding heat (energy) to one group of atoms (hot reservoir) -and subtracting heat from another (cold reservoir). E.g. a simulation -sampling from the McDLT ensemble. -

    -

    If the region keyword is used, the atom must be in both the group -and the specified geometric region in order to have -energy added or subtracted to it. If not specified, then the atoms in -the group are affected wherever they may move to. -

    -

    Heat addition/subtraction is performed every N timesteps. The eflux -parameter can be specified as a numeric constant or as a variable (see -below). If it is a numeric constant or equal-style variable which -evaluates to a scalar value, then the eflux determines the change in -aggregate energy of the entire group of atoms per unit time, e.g. in -eV/psec for metal units. In this case it is an -"extensive" quantity, meaning its magnitude should be scaled with the -number of atoms in the group. Note that since eflux has per-time -units (i.e. it is a flux), this means that a larger value of N will -add/subtract a larger amount of energy each time the fix is invoked. -

    -

    If eflux is specified as an atom-style variable (see below), then -the variable computes one value per atom. In this case, each value is -the energy flux for a single atom, again in units of energy per unit -time. In this case, each value is an "intensive" quantity, which need -not be scaled with the number of atoms in the group. -

    -

    As mentioned above, the eflux parameter can be specified as an -equal-style or atom_style variable. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value(s) used to determine the flux. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent flux. -

    -

    Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent flux -with optional time-dependence as well. -

    -

    IMPORTANT NOTE: If heat is subtracted from the system too aggressively -so that the group's kinetic energy would go to zero, or any individual -atom's kinetic energy would go to zero for the case where eflux is -an atom-style variable, then LAMMPS will halt with an error message. -

    -

    Fix heat is different from a thermostat such as fix nvt -or fix temp/rescale in that energy is -added/subtracted continually. Thus if there isn't another mechanism -in place to counterbalance this effect, the entire system will heat or -cool continuously. You can use multiple heat fixes so that the net -energy change is 0.0 or use fix viscous to drain -energy from the system. -

    -

    This fix does not change the coordinates of its atoms; it only scales -their velocities. Thus you must still use an integration fix -(e.g. fix nve) on the affected atoms. This fix should -not normally be used on atoms that have their temperature controlled -by another fix - e.g. fix nvt or fix -langevin fix. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. This scalar is the -most recent value by which velocites were scaled. The scalar value -calculated by this fix is "intensive". If eflux is specified as -an atom-style variable, this fix computes the average value by which -the velocities were scaled for all of the atoms that had their -velocities scaled. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute temp, compute -temp/region -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_imd.html b/doc/doc2/fix_imd.html deleted file mode 100644 index 1d89148879..0000000000 --- a/doc/doc2/fix_imd.html +++ /dev/null @@ -1,172 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix imd command -

    -

    Syntax: -

    -
    fix ID group-ID imd trate port keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • imd = style name of this fix command - -
    • port = port number on which the fix listens for an IMD client - -
    • keyword = unwrap or fscale or trate - -
        unwrap arg = on or off
-    off = coordinates are wrapped back into the principal unit cell (default)
-    on = "unwrapped" coordinates using the image flags used
-  fscale arg = factor
-    factor = floating point number to scale IMD forces (default: 1.0)
-  trate arg = transmission rate of coordinate data sets (default: 1)
-  nowait arg = on or off
-    off = LAMMPS waits to be connected to an IMD client before continuing (default)
-    on = LAMMPS listens for an IMD client, but continues with the run 
-
      - -
    -

    Examples: -

    -
    fix vmd all imd 5678 
-fix comm all imd 8888 trate 5 unwrap on fscale 10.0 
-
    -

    Description: -

    -

    This fix implements the "Interactive MD" (IMD) protocol which allows -realtime visualization and manipulation of MD simulations through the -IMD protocol, as initially implemented in VMD and NAMD. Specifically -it allows LAMMPS to connect an IMD client, for example the VMD -visualization program, so that it can monitor the progress of the -simulation and interactively apply forces to selected atoms. -

    -

    If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD -then fix imd will use POSIX threads to spawn a IMD communication -thread on MPI rank 0 in order to offload data reading and writing -from the main execution thread and potentially lower the inferred -latencies for slow communication links. This feature has only been -tested under linux. -

    -

    There are example scripts for using this package with LAMMPS in -examples/USER/imd. Additional examples and a driver for use with the -Novint Falcon game controller as haptic device can be found at: -http://sites.google.com/site/akohlmey/software/vrpn-icms. -

    -

    The source code for this fix includes code developed by the -Theoretical and Computational Biophysics Group in the Beckman -Institute for Advanced Science and Technology at the University of -Illinois at Urbana-Champaign. We thank them for providing a software -interface that allows codes like LAMMPS to hook to VMD. -

    -

    Upon initialization of the fix, it will open a communication port on -the node with MPI task 0 and wait for an incoming connection. As soon -as an IMD client is connected, the simulation will continue and the -fix will send the current coordinates of the fix's group to the IMD -client at every trate MD step. When using r-RESPA, trate applies to -the steps of the outmost RESPA level. During a run with an active IMD -connection also the IMD client can request to apply forces to selected -atoms of the fix group. -

    -

    The port number selected must be an available network port number. On -many machines, port numbers < 1024 are reserved for accounts with -system manager privilege and specific applications. If multiple imd -fixes would be active at the same time, each needs to use a different -port number. -

    -

    The nowait keyword controls the behavior of the fix when no IMD -client is connected. With the default setting of off, LAMMPS will -wait until a connection is made before continuing with the -execution. Setting nowait to on will have the LAMMPS code be ready -to connect to a client, but continue with the simulation. This can for -example be used to monitor the progress of an ongoing calculation -without the need to be permanently connected or having to download a -trajectory file. -

    -

    The trate keyword allows to select how often the coordinate data is -sent to the IMD client. It can also be changed on request of the IMD -client through an IMD protocol message. The unwrap keyword allows -to send "unwrapped" coordinates to the IMD client that undo the -wrapping back of coordinates into the principle unit cell, as done by -default in LAMMPS. The fscale keyword allows to apply a scaling -factor to forces transmitted by the IMD client. The IMD protocols -stipulates that forces are transferred in kcal/mol/angstrom under the -assumption that coordinates are given in angstrom. For LAMMPS runs -with different units or as a measure to tweak the forces generated by -the manipulation of the IMD client, this option allows to make -adjustments. -

    -

    To connect VMD to a listening LAMMPS simulation on the same machine -with fix imd enabled, one needs to start VMD and load a coordinate or -topology file that matches the fix group. When the VMD command -prompts appears, one types the command line: -

    -
    imd connect localhost 5678 
-
    -

    This assumes that fix imd was started with 5678 as a port -number for the IMD protocol. -

    -

    The steps to do interactive manipulation of a running simulation in -VMD are the following: -

    -

    In the Mouse menu of the VMD Main window, select "Mouse -> Force -> -Atom". You may alternately select "Residue", or "Fragment" to apply -forces to whole residues or fragments. Your mouse can now be used to -apply forces to your simulation. Click on an atom, residue, or -fragment and drag to apply a force. Click quickly without moving the -mouse to turn the force off. You can also use a variety of 3D position -trackers to apply forces to your simulation. Game controllers or haptic -devices with force-feedback such as the Novint Falcon or Sensable -PHANTOM allow you to feel the resistance due to inertia or interactions -with neighbors that the atoms experience you are trying to move, as if -they were real objects. See the VMD IMD Homepage and the -VRPN-ICMS Homepage for more details. -

    -

    If IMD control messages are received, a line of text describing the -message and its effect will be printed to the LAMMPS output screen, if -screen output is active. -

    - - - - - - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    When used in combination with VMD, a topology or coordinate file has -to be loaded, which matches (in number and ordering of atoms) the -group the fix is applied to. The fix internally sorts atom IDs by -ascending integer value; in VMD (and thus the IMD protocol) those will -be assigned 0-based consecutive index numbers. -

    -

    When using multiple active IMD connections at the same time, each -needs to use a different port number. -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_indent.html b/doc/doc2/fix_indent.html deleted file mode 100644 index 701a576664..0000000000 --- a/doc/doc2/fix_indent.html +++ /dev/null @@ -1,212 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix indent command -

    -

    Syntax: -

    -
    fix ID group-ID indent K keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • indent = style name of this fix command - -
    • K = force constant for indenter surface (force/distance^2 units) - -
    • one or more keyword/value pairs may be appended - -
    • keyword = sphere or cylinder or plane or side or units - -
        sphere args = x y z R
-    x,y,z = initial position of center of indenter (distance units)
-    R = sphere radius of indenter (distance units)
-    any of x,y,z,R can be a variable (see below)
-  cylinder args = dim c1 c2 R
-    dim = x or y or z = axis of cylinder
-    c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
-    R = cylinder radius of indenter (distance units)
-    any of c1,c2,R can be a variable (see below)
-  plane args = dim pos side
-    dim = x or y or z = plane perpendicular to this dimension
-    pos = position of plane in dimension x, y, or z (distance units)
-    pos can be a variable (see below)
-    side = lo or hi
-  side value = in or out
-    in = the indenter acts on particles inside the sphere or cylinder
-    out = the indenter acts on particles outside the sphere or cylinder
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
-fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
-fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box 
-
    -

    Description: -

    -

    Insert an indenter within a simulation box. The indenter repels all -atoms in the group that touch it, so it can be used to push into a -material or as an obstacle in a flow. Or it can be used as a -constraining wall around a simulation; see the discussion of the -side keyword below. -

    -

    The indenter can either be spherical or cylindrical or planar. You -must set one of those 3 keywords. -

    -

    A spherical indenter exerts a force of magnitude -

    -
    F(r) = - K (r - R)^2 
-
    -

    on each atom where K is the specified force constant, r is the -distance from the atom to the center of the indenter, and R is the -radius of the indenter. The force is repulsive and F(r) = 0 for r > -R. -

    -

    A cylindrical indenter exerts the same force, except that r is the -distance from the atom to the center axis of the cylinder. The -cylinder extends infinitely along its axis. -

    -

    Spherical and cylindrical indenters account for periodic boundaries in -two ways. First, the center point of a spherical indenter (x,y,z) or -axis of a cylindrical indenter (c1,c2) is remapped back into the -simulation box, if the box is periodic in a particular dimension. -This occurs every timestep if the indenter geometry is specified with -a variable (see below), e.g. it is moving over time. Second, the -calculation of distance to the indenter center or axis accounts for -periodic boundaries. Both of these mean that an indenter can -effectively move through and straddle one or more periodic boundaries. -

    -

    A planar indenter is really an axis-aligned infinite-extent wall -exerting the same force on atoms in the system, where R is the -position of the plane and r-R is the distance from the plane. If -the side parameter of the plane is specified as lo then it will -indent from the lo end of the simulation box, meaning that atoms with -a coordinate less than the plane's current position will be pushed -towards the hi end of the box and atoms with a coordinate higher than -the plane's current position will feel no force. Vice versa if side -is specified as hi. -

    -

    Any of the 4 quantities defining a spherical indenter's geometry can -be specified as an equal-style variable, namely x, -y, z, or R. Similarly, for a cylindrical indenter, any of c1, -c2, or R, can be a variable. For a planar indenter, pos can be -a variable. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to define the -indenter geometry. -

    -

    Note that equal-style variables can specify formulas with various -mathematical functions, and include thermo_style -command keywords for the simulation box parameters and timestep and -elapsed time. Thus it is easy to specify indenter properties that -change as a function of time or span consecutive runs in a continuous -fashion. For the latter, see the start and stop keywords of the -run command and the elaplong keyword of thermo_style -custom for details. -

    -

    For example, if a spherical indenter's x-position is specfied as v_x, -then this variable definition will keep it's center at a relative -position in the simulation box, 1/4 of the way from the left edge to -the right edge, even if the box size changes: -

    -
    variable x equal "xlo + 0.25*lx" 
-
    -

    Similarly, either of these variable definitions will move the indenter -from an initial position at 2.5 at a constant velocity of 5: -

    -
    variable x equal "2.5 + 5*elaplong*dt"
-variable x equal vdisplace(2.5,5) 
-
    -

    If a spherical indenter's radius is specified as v_r, then these -variable definitions will grow the size of the indenter at a specfied -rate. -

    -
    variable r0 equal 0.0
-variable rate equal 1.0
-variable r equal "v_r0 + step*dt*v_rate" 
-
    -

    If the side keyword is specified as out, which is the default, -then particles outside the indenter are pushded away from its outer -surface, as described above. This only applies to spherical or -cylindrical indenters. If the side keyword is specified as in, -the action of the indenter is reversed. Particles inside the indenter -are pushed away from its inner surface. In other words, the indenter -is now a containing wall that traps the particles inside it. If the -radius shrinks over time, it will squeeze the particles. -

    -

    The units keyword determines the meaning of the distance units used -to define the indenter geometry. A box value selects standard -distance units as defined by the units command, -e.g. Angstroms for units = real or metal. A lattice value means the -distance units are in lattice spacings. The lattice -command must have been previously used to define the lattice spacing. -The (x,y,z) coords of the indenter position are scaled by the x,y,z -lattice spacings respectively. The radius of a spherical or -cylindrical indenter is scaled by the x lattice spacing. -

    -

    Note that the units keyword only affects indenter geometry parameters -specified directly with numbers, not those specified as variables. In -the latter case, you should use the xlat, ylat, zlat keywords of -the thermo_style command if you want to include -lattice spacings in a variable formula. -

    -

    The force constant K is not affected by the units keyword. It is -always in force/distance^2 units where force and distance are defined -by the units command. If you wish K to be scaled by the -lattice spacing, you can define K with a variable whose formula -contains xlat, ylat, zlat keywords of the -thermo_style command, e.g. -

    -
    variable k equal 100.0/xlat/xlat
-fix 1 all indent $k sphere ... 
-
    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the energy of interaction between atoms and the indenter to -the system's potential energy as part of thermodynamic -output. The energy of each particle interacting -with the indenter is K/3 (r - R)^3. -

    -

    This fix computes a global scalar energy and a global 3-vector of -forces (on the indenter), which can be accessed by various output -commands. The scalar and vector values -calculated by this fix are "extensive". -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. Note that if you -define the indenter geometry with a variable using a time-dependent -formula, LAMMPS uses the iteration count in the minimizer as the -timestep. But it is almost certainly a bad idea to have the indenter -change its position or size during a minimization. LAMMPS does not -check if you have done this. -

    -

    IMPORTANT NOTE: If you want the atom/indenter interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you must enable the fix_modify -energy option for this fix. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: -

    -

    The option defaults are side = out and units = lattice. -

    - diff --git a/doc/doc2/fix_ipi.html b/doc/doc2/fix_ipi.html deleted file mode 100644 index 1c76f7af28..0000000000 --- a/doc/doc2/fix_ipi.html +++ /dev/null @@ -1,98 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ipi command -

    -

    Syntax: -

    -
    fix ID group-ID ipi address port [unix] 
-
    -
    • ID, group-ID are documented in fix command -
    • ipi = style name of this fix command -
    • address = internet address (FQDN or IP), or UNIX socket name -
    • port = port number (ignored for UNIX sockets) -
    • optional keyword = unix, if present uses a unix socket -
    -

    Examples: -

    -

    fix 1 all ipi my.server.com 12345 -fix 1 all ipi mysocket 666 unix -

    -

    Description: -

    -

    This fix enables LAMMPS to be run as a client for the i-PI Python -wrapper (IPI) for performing a path integral molecular dynamics -(PIMD) simulation. The philosophy behind i-PI is described in the -following publication (IPI-CPC). -

    -

    A version of the i-PI package, containing only files needed for use -with LAMMPS, is provided in the tools/i-pi directory. See the -tools/i-pi/manual.pdf for an introduction to i-PI. The -examples/USER/i-pi directory contains example scripts for using i-PI -with LAMMPS. -

    -

    In brief, the path integral molecular dynamics is performed by the -Python wrapper, while the client (LAMMPS in this case) simply computes -forces and energy for each configuration. The communication between -the two components takes place using sockets, and is reduced to the -bare minimum. All the parameters of the dynamics are specified in the -input of i-PI, and all the parameters of the force field must be -specified as LAMMPS inputs, preceding the fix ipi command. -

    -

    The server address must be specified by the address argument, and -can be either the IP address, the fully-qualified name of the server, -or the name of a UNIX socket for local, faster communication. In the -case of internet sockets, the port argument specifies the port -number on which i-PI is listening, while the unix optional switch -specifies that the socket is a UNIX socket. -

    -

    Note that there is no check of data integrity, or that the atomic -configurations make sense. It is assumed that the species in the i-PI -input are listed in the same order as in the data file of LAMMPS. The -initial configuration is ignored, as it will be substituted with the -coordinates received from i-PI before forces are ever evaluated. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    There is no restart information associated with this fix, since all -the dynamical parameters are dealt with by i-PI. -

    -

    Restrictions: -

    -

    Using this fix on anything other than all atoms requires particular -care, since i-PI will know nothing on atoms that are not those whose -coordinates are transferred. However, one could use this strategy to -define an external potential acting on the atoms that are moved by -i-PI. -

    -

    This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. Because of -the use of UNIX domain sockets, this fix will only work in a UNIX -environment. -

    -

    Related commands: -

    -

    fix nve -

    -
    - - - -

    (IPI-CPC) Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, -1019-1026 (2014). -

    - - -

    (IPI) -http://epfl-cosmo.github.io/gle4md/index.html?page=ipi -

    - diff --git a/doc/doc2/fix_langevin.html b/doc/doc2/fix_langevin.html deleted file mode 100644 index 78687927d9..0000000000 --- a/doc/doc2/fix_langevin.html +++ /dev/null @@ -1,362 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix langevin command -

    -

    fix langevin/kk command -

    -

    Syntax: -

    -
    fix ID group-ID langevin Tstart Tstop damp seed keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • langevin = style name of this fix command - -
    • Tstart,Tstop = desired temperature at start/end of run (temperature units) - -
    • Tstart can be a variable (see below) - -
    • damp = damping parameter (time units) - -
    • seed = random number seed to use for white noise (positive integer) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = angmom or omega or scale or tally or zero - -
        angmom value = no or scale
-    no = do not thermostat rotational degrees of freedom via the angular momentum
-    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
-  gjf value = no or yes
-    no = use standard formulation
-    yes = use Gronbech-Jensen/Farago formulation
-  omega value = no or yes
-    no = do not thermostat rotational degrees of freedom via the angular velocity
-    yes = do thermostat rotational degrees of freedom via the angular velocity
-  scale values = type ratio
-    type = atom type (1-N)
-    ratio = factor by which to scale the damping coefficient
-  tally value = no or yes
-    no = do not tally the energy added/subtracted to atoms
-    yes = do tally the energy added/subtracted to atoms
-  zero value = no or yes
-    no = do not set total random force to zero
-    yes = set total random force to zero 
-
      - -
    -

    Examples: -

    -
    fix 3 boundary langevin 1.0 1.0 1000.0 699483
-fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5
-fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333 
-
    -

    Description: -

    -

    Apply a Langevin thermostat as described in (Schneider) -to a group of atoms which models an interaction with a background -implicit solvent. Used with fix nve, this command -performs Brownian dynamics (BD), since the total force on each atom -will have the form: -

    -
    F = Fc + Ff + Fr
-Ff = - (m / damp) v
-Fr is proportional to sqrt(Kb T m / (dt damp)) 
-
    -

    Fc is the conservative force computed via the usual inter-particle -interactions (pair_style, -bond_style, etc). -

    -

    The Ff and Fr terms are added by this fix on a per-particle basis. -See the pair_style dpd/tstat command for a -thermostatting option that adds similar terms on a pairwise basis to -pairs of interacting particles. -

    -

    Ff is a frictional drag or viscous damping term proportional to the -particle's velocity. The proportionality constant for each atom is -computed as m/damp, where m is the mass of the particle and damp is -the damping factor specified by the user. -

    -

    Fr is a force due to solvent atoms at a temperature T randomly bumping -into the particle. As derived from the fluctuation/dissipation -theorem, its magnitude as shown above is proportional to sqrt(Kb T m / -dt damp), where Kb is the Boltzmann constant, T is the desired -temperature, m is the mass of the particle, dt is the timestep size, -and damp is the damping factor. Random numbers are used to randomize -the direction and magnitude of this force as described in -(Dunweg), where a uniform random number is used (instead of -a Gaussian random number) for speed. -

    -

    Note that unless you use the omega or angmom keywords, the -thermostat effect of this fix is applied to only the translational -degrees of freedom for the particles, which is an important -consideration for finite-size particles, which have rotational degrees -of freedom, are being thermostatted. The translational degrees of -freedom can also have a bias velocity removed from them before -thermostatting takes place; see the description below. -

    -

    IMPORTANT NOTE: Unlike the fix nvt command which -performs Nose/Hoover thermostatting AND time integration, this fix -does NOT perform time integration. It only modifies forces to effect -thermostatting. Thus you must use a separate time integration fix, -like fix nve to actually update the velocities and -positions of atoms using the modified forces. Likewise, this fix -should not normally be used on atoms that also have their temperature -controlled by another fix - e.g. by fix nvt or fix -temp/rescale commands. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. -

    -

    Tstart can be specified as an equal-style or atom-style -variable. In this case, the Tstop setting is -ignored. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -target temperature. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. -

    -

    Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent -temperature with optional time-dependence as well. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that remove a "bias" from the -atom velocities. E.g. removing the center-of-mass velocity from a -group of atoms or removing the x-component of velocity from the -calculation. This is not done by default, but only if the -fix_modify command is used to assign a temperature -compute to this fix that includes such a bias term. See the doc pages -for individual compute commands to determine which ones -include a bias. In this case, the thermostat works in the following -manner: bias is removed from each atom, thermostatting is performed on -the remaining thermal degrees of freedom, and the bias is added back -in. -

    -

    The damp parameter is specified in time units and determines how -rapidly the temperature is relaxed. For example, a value of 100.0 -means to relax the temperature in a timespan of (roughly) 100 time -units (tau or fmsec or psec - see the units command). -The damp factor can be thought of as inversely related to the -viscosity of the solvent. I.e. a small relaxation time implies a -hi-viscosity solvent and vice versa. See the discussion about gamma -and viscosity in the documentation for the fix -viscous command for more details. -

    -

    The random # seed must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random numbers. -Thus the dynamics of the system will not be identical on two runs on -different numbers of processors. -

    -
    - -

    The keyword/value option pairs are used in the following ways. -

    -

    The keyword angmom and omega keywords enable thermostatting of -rotational degrees of freedom in addition to the usual translational -degrees of freedom. This can only be done for finite-size particles. -

    -

    A simulation using atom_style sphere defines an omega for finite-size -spheres. A simulation using atom_style ellipsoid defines a finite -size and shape for aspherical particles and an angular momentum. -The Langevin formulas for thermostatting the rotational degrees of -freedom are the same as those above, where force is replaced by -torque, m is replaced by the moment of inertia I, and v is replaced by -omega (which is derived from the angular momentum in the case of -aspherical particles). -

    -

    The rotational temperature of the particles can be monitored by the -compute temp/sphere and compute -temp/asphere commands with their rotate -options. -

    -

    For the omega keyword there is also a scale factor of 10.0/3.0 that -is applied as a multiplier on the Ff (damping) term in the equation -above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does -not affect the thermostatting behaviour of the Langevin formalism but -insures that the randomized rotational diffusivity of spherical -particles is correct. -

    -

    For the angmom keyword a similar scale factor is needed which is -10.0/3.0 for spherical particles, but is anisotropic for aspherical -particles (e.g. ellipsoids). Currently LAMMPS only applies an -isotropic scale factor, and you can choose its magnitude as the -specified value of the angmom keyword. If your aspherical particles -are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good -choice. If they are highly aspherical, a value of 1.0 is as good a -choice as any, since the effects on rotational diffusivity of the -particles will be incorrect regardless. Note that for any reasonable -scale factor, the thermostatting effect of the angmom keyword on the -rotational temperature of the aspherical particles should still be -valid. -

    -

    The keyword scale allows the damp factor to be scaled up or down by -the specified factor for atoms of that type. This can be useful when -different atom types have different sizes or masses. It can be used -multiple times to adjust damp for several atom types. Note that -specifying a ratio of 2 increases the relaxation time which is -equivalent to the solvent's viscosity acting on particles with 1/2 the -diameter. This is the opposite effect of scale factors used by the -fix viscous command, since the damp factor in fix -langevin is inversely related to the gamma factor in fix viscous. -Also note that the damping factor in fix langevin includes the -particle mass in Ff, unlike fix viscous. Thus the mass and size of -different atom types should be accounted for in the choice of ratio -values. -

    -

    The keyword tally enables the calculation of the cumulative energy -added/subtracted to the atoms as they are thermostatted. Effectively -it is the energy exchanged between the infinite thermal reservoir and -the particles. As described below, this energy can then be printed -out or added to the potential energy of the system to monitor energy -conservation. -

    -

    IMPORTANT NOTE: this accumulated energy does NOT include kinetic -energy removed by the zero flag. LAMMPS will print a warning when -both options are active. -

    -

    The keyword zero can be used to eliminate drift due to the -thermostat. Because the random forces on different atoms are -independent, they do not sum exactly to zero. As a result, this fix -applies a small random force to the entire system, and the -center-of-mass of the system undergoes a slow random walk. If the -keyword zero is set to yes, the total random force is set exactly -to zero by subtracting off an equal part of it from each atom in the -group. As a result, the center-of-mass of a system with zero initial -momentum will not drift over time. -

    -

    The keyword gjf can be used to run the Gronbech-Jensen/Farago - time-discretization of the Langevin model. As -described in the papers cited below, the purpose of this method is to -enable longer timesteps to be used (up to the numerical stability -limit of the integrator), while still producing the correct Boltzmann -distribution of atom positions. It is implemented within LAMMPS, by -changing how the the random force is applied so that it is composed of -the average of two random forces representing half-contributions from -the previous and current time intervals. -

    -

    In common with all methods based on Verlet integration, the -discretized velocities generated by this method in conjunction with -velocity-Verlet time integration are not exactly conjugate to the -positions. As a result the temperature (computed from the discretized -velocities) will be systematically lower than the target temperature, -by a small amount which grows with the timestep. Nonetheless, the -distribution of atom positions will still be consistent with the -target temperature. -

    -

    As an example of using the gjf keyword, for molecules containing C-H -bonds, configurational properties generated with dt = 2.5 fs and tdamp -= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity -distribution systematically decreases with increasing timestep, the -method should not be used to generate properties that depend on the -velocity distribution, such as the velocity autocorrelation function -(VACF). In this example, the velocity distribution at dt = 2.5fs -generates an average temperature of 220 K, instead of 300 K. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a temperature compute -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Langevin thermostatting to the -system's potential energy as part of thermodynamic -output. Note that use of this option requires -setting the tally keyword to yes. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". Note that calculation of this -quantity requires setting the tally keyword to yes. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix nvt, fix temp/rescale, fix -viscous, fix nvt, pair_style -dpd/tstat -

    -

    Default: -

    -

    The option defaults are angmom = no, omega = no, scale = 1.0 for all -types, tally = no, zero = no, gjf = no. -

    -
    - - - -

    (Dunweg) Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). -

    - - -

    (Schneider) Schneider and Stoll, Phys Rev B, 17, 1302 (1978). -

    - - -

    (Gronbech-Jensen) Gronbech-Jensen and Farago, Mol Phys, 111, 983 -(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, -185, 524 (2014) -

    - diff --git a/doc/doc2/fix_langevin_drude.html b/doc/doc2/fix_langevin_drude.html deleted file mode 100644 index a118f323c6..0000000000 --- a/doc/doc2/fix_langevin_drude.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix langevin/drude command -

    -

    Syntax: -

    -
    fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • langevin/drude = style name of this fix command - -
    • Tcom = desired temperature of the centers of mass (temperature units) - -
    • damp_com = damping parameter for the thermostat on centers of mass (time units) - -
    • seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer) - -
    • Tdrude = desired temperature of the Drude oscillators (temperature units) - -
    • damp_drude = damping parameter for the thermostat on Drude oscillators (time units) - -
    • seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = zero - -
        zero value = no or yes
-    no = do not set total random force on centers of mass to zero
-    yes = set total random force on centers of mass to zero 
-
      - -
    -

    Examples: -

    -
    fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
-fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes 
-
    -

    Description: -

    -

    Apply two Langevin thermostats as described in (Jiang) for -thermalizing the reduced degrees of freedom of Drude oscillators. -This link describes how to use the thermalized Drude oscillator -model in LAMMPS and polarizable models in LAMMPS -are discussed in this Section. -

    -

    Drude oscillators are a way to simulate polarizables atoms, by -splitting them into a core and a Drude particle bound by a harmonic -bond. The thermalization works by transforming the particles degrees -of freedom by these equations. In these equations upper case denotes -atomic or center of mass values and lower case denotes Drude particle -or dipole values. Primes denote the transformed (reduced) values, -while bare letters denote the original values. -

    -Velocities: -\begin{equation} V' = \frac {M\, V + m\, v} {M'} \end{equation} -\begin{equation} v' = v - V \end{equation} -Masses: -\begin{equation} M' = M + m \end{equation} -\begin{equation} m' = \frac {M\, m } {M'} \end{equation} -The Langevin forces are computed as -\begin{equation} F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' \end{equation} -\begin{equation} f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' \end{equation} -\(F_r'\) is a random force proportional to -\(\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} - {\mathrm dt\, \mathtt{damp\_com} } - } \). -
    -\(f_r'\) is a random force proportional to -\(\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'} - {\mathrm dt\, \mathtt{damp\_drude} } - } \). -
    -

    Then the real forces acting on the particles are computed from the inverse -transform: -\begin{equation} F = \frac M {M'}\, F' - f' \end{equation} -\begin{equation} f = \frac m {M'}\, F' + f' \end{equation} -

    -

    This fix also thermostates non-polarizable atoms in the group at -temperature Tcom, as if they had a massless Drude partner. The -Drude particles themselves need not be in the group. The center of -mass and the dipole are thermostated iff the core atom is in the -group. -

    -

    Note that the thermostat effect of this fix is applied to only the -translational degrees of freedom of the particles, which is an -important consideration if finite-size particles, which have -rotational degrees of freedom, are being thermostated. The -translational degrees of freedom can also have a bias velocity removed -from them before thermostating takes place; see the description below. -

    -

    IMPORTANT NOTE: Like the fix langevin command, -this fix does NOT perform time integration. It only modifies forces to -effect thermostating. Thus you must use a separate time integration -fix, like fix nve or fix nph to actually -update the velocities and positions of atoms using the modified -forces. Likewise, this fix should not normally be used on atoms that -also have their temperature controlled by another fix - e.g. by fix -nvt or fix temp/rescale commands. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostating. -

    -
    - -

    This fix requires each atom know whether it is a Drude particle or -not. You must therefore use the fix drude command to -specify the Drude status of each atom type. -

    -

    IMPORTANT NOTE: only the Drude core atoms need to be in the group -specified for this fix. A Drude electron will be transformed together -with its cores even if it is not itself in the group. It is safe to -include Drude electrons or non-polarizable atoms in the group. The -non-polarizable atoms will simply not be thermostatted as if they had -a massless Drude partner (electron). -

    -

    IMPORTANT NOTE: Ghost atoms need to know their velocity for this fix -to act correctly. You must use the comm_modify -command to enable this, e.g. -

    -
    comm_modify vel yes 
-
    -
    - -

    Tcom is the target temperature of the centers of mass, which would -be used to thermostate the non-polarizable atoms. Tdrude is the -(normally low) target temperature of the core-Drude particle pairs -(dipoles). Tcom and Tdrude can be specified as an equal-style -variable. If the value is a variable, it should be -specified as v_name, where name is the variable name. In this case, -the variable will be evaluated each timestep, and its value used to -determine the target temperature. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. -

    -

    Like other fixes that perform thermostating, this fix can be used with -compute commands that remove a "bias" from the atom -velocities. E.g. removing the center-of-mass velocity from a group of -atoms. This is not done by default, but only if the -fix_modify command is used to assign a temperature -compute to this fix that includes such a bias term. See the doc pages -for individual compute commands to determine which ones -include a bias. In this case, the thermostat works in the following -manner: bias is removed from each atom, thermostating is performed on -the remaining thermal degrees of freedom, and the bias is added back -in. NOTE: this feature has not been tested. -

    -

    Note: The temperature thermostating the core-Drude particle pairs -should be chosen low enough, so as to mimic as closely as possible the -self-consistent minimization. It must however be high enough, so that -the dipoles can follow the local electric field exerted by the -neighbouring atoms. The optimal value probably depends on the -temperature of the centers of mass and on the mass of the Drude -particles. -

    -

    damp_com is the characteristic time for reaching thermal equilibrium -of the centers of mass. For example, a value of 100.0 means to relax -the temperature of the centers of mass in a timespan of (roughly) 100 -time units (tau or fmsec or psec - see the units -command). damp_drude is the characteristic time for reaching -thermal equilibrium of the dipoles. It is typically a few timesteps. -

    -

    The number seed_com and seed_drude are positive integers. They set -the seeds of the Marsaglia random number generators used for -generating the random forces on centers of mass and on the -dipoles. Each processor uses the input seed to generate its own unique -seed and its own stream of random numbers. Thus the dynamics of the -system will not be identical on two runs on different numbers of -processors. -

    -

    The keyword zero can be used to eliminate drift due to the -thermostat on centers of mass. Because the random forces on different -centers of mass are independent, they do not sum exactly to zero. As -a result, this fix applies a small random force to the entire system, -and the momentum of the total center of mass of the system undergoes a -slow random walk. If the keyword zero is set to yes, the total -random force on the centers of mass is set exactly to zero by -subtracting off an equal part of it from each center of mass in the -group. As a result, the total center of mass of a system with zero -initial momentum will not drift over time. -

    -

    The actual temperatures of cores and Drude particles, in -center-of-mass and relatice coordinates, respectively, can be -calculated using the compute temp/drude -command. -

    -
    - -

    Usage example for rigid bodies in the NPT ensemble: -

    -
    comm_modify vel yes
-fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
-fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
-fix NVE DRUDES nve
-thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TATOM c_TDRUDE f_TEMP[1] f_TEMP[2] 
-
    -

    Comments: -

    -
    • Drude particles should not be in the rigid group, otherwise the Drude -
    • oscillators will be frozen and the system will lose its -
    • polarizability. zero yes avoids a drift of the center of mass of -
    • the system, but is a bit slower. use two different random seeds to -
    • avoid unphysical correlations. temperature is controlled by the fix -
    • langevin/drude, so the time-integration fixes do not thermostate. -
    • don't forget to time-integrate both cores and Drude particles. -
    • pressure is time-integrated only once by using nve for Drude -
    • particles and nph for atoms/cores (or vice versa). Do not use nph -
    • for both. contrary to the alternative thermostating using Nose-Hoover -
    • thermostat fix npt and fix drude/transform, the fix_modify -
    • command is not required here, because the fix nph computes the -
    • global pressure even if its group is ATOMS. This is what we want. If -
    • we thermostated ATOMS using npt, the pressure should be the global -
    • one, but the temperature should be only that of the cores. That's why -
    • the command fix_modify should be called in that case. f_TEMP[1] -
    • and f_TEMP[2] contain the reduced temperatures of the cores/atoms -
    • and of the Drude particles (see below). They should be 300. and 1. on -
    • average here. -
    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a temperature compute -you have defined to this fix which will be used in its thermostating -procedure, as described above. For consistency, the group used by the -compute should include the group of this fix and the Drude particles. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix langevin, -fix drude, -fix drude/transform, -compute temp/drude, -pair_style thole -

    -

    Default: -

    -

    The option defaults are zero = no. -

    -
    - - - -

    (Jiang) Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J -Phys Chem Lett, 2, 87-92 (2011). -

    - diff --git a/doc/doc2/fix_langevin_eff.html b/doc/doc2/fix_langevin_eff.html deleted file mode 100644 index c2b8617da9..0000000000 --- a/doc/doc2/fix_langevin_eff.html +++ /dev/null @@ -1,128 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix langevin/eff command -

    -

    Syntax: -

    -
    fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • langevin/eff = style name of this fix command - -
    • Tstart,Tstop = desired temperature at start/end of run (temperature units) - -
    • damp = damping parameter (time units) - -
    • seed = random number seed to use for white noise (positive integer) - -
    • zero or more keyword/value pairs may be appended - -
      keyword = scale or tally or zero
-  scale values = type ratio
-    type = atom type (1-N)
-    ratio = factor by which to scale the damping coefficient
-  tally values = no or yes
-    no = do not tally the energy added/subtracted to atoms
-    yes = do tally the energy added/subtracted to atoms 
-
      -
        zero value = no or yes
-    no = do not set total random force to zero
-    yes = set total random force to zero 
-
      - -
    -

    Examples: -

    -
    fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
-fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 
-
    -

    Description: -

    -

    Apply a Langevin thermostat as described in (Schneider) -to a group of nuclei and electrons in the electron force -field model. Used with fix nve/eff, -this command performs Brownian dynamics (BD), since the total force on -each atom will have the form: -

    -
    F = Fc + Ff + Fr
-Ff = - (m / damp) v
-Fr is proportional to sqrt(Kb T m / (dt damp)) 
-
    -

    Fc is the conservative force computed via the usual inter-particle -interactions (pair_style). -

    -

    The Ff and Fr terms are added by this fix on a per-particle basis. -

    -

    The operation of this fix is exactly like that described by the fix -langevin command, except that the thermostatting -is also applied to the radial electron velocity for electron -particles. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a temperature compute -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Langevin thermostatting to the -system's potential energy as part of thermodynamic -output. Note that use of this option requires -setting the tally keyword to yes. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". Note that calculation of this -quantity requires setting the tally keyword to yes. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix langevin -

    -

    Default: -

    -

    The option defaults are scale = 1.0 for all types and tally = no. -

    -
    - - - -

    (Dunweg) Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). -

    - - -

    (Schneider) Schneider and Stoll, Phys Rev B, 17, 1302 (1978). -

    - diff --git a/doc/doc2/fix_lb_fluid.html b/doc/doc2/fix_lb_fluid.html deleted file mode 100644 index 090c688753..0000000000 --- a/doc/doc2/fix_lb_fluid.html +++ /dev/null @@ -1,388 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix lb/fluid command -

    -

    Syntax: -

    -
    fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • lb/fluid = style name of this fix command - -
    • nevery = update the lattice-Boltzmann fluid every this many timesteps - -
    • LBtype = 1 to use the standard finite difference LB integrator, -2 to use the LB integrator of Ollila et al. - -
    • viscosity = the fluid viscosity (units of mass/(time*length)). - -
    • density = the fluid density. - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = setArea or setGamma or scaleGamma or dx or dm or a0 or noise or calcforce or trilinear or D3Q19 or read_restart or write_restart or zwall_velocity or bodyforce or printfluid - -
        setArea values = type node_area
-      type = atom type (1-N)
-      node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
-  setGamma values = gamma
-      gamma = user set value for the force coupling constant.
-  scaleGamma values = type gammaFactor
-      type = atom type (1-N)
-      gammaFactor = factor to scale the setGamma gamma value by, for the specified atom type.    
-  dx values = dx_LB = the lattice spacing.
-  dm values = dm_LB = the lattice-Boltzmann mass unit.
-  a0 values = a_0_real = the square of the speed of sound in the fluid.
-  noise values = Temperature seed 
-      Temperature = fluid temperature. 
-      seed = random number generator seed (positive integer) 
-  calcforce values = N forcegroup-ID 
-      N = output the force and torque every N timesteps
-      forcegroup-ID = ID of the particle group to calculate the force and torque of
-  trilinear values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
-  D3Q19 values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
-  read_restart values = restart file = name of the restart file to use to restart a fluid run.
-  write_restart values = N = write a restart file every N MD timesteps.
-  zwall_velocity values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
-  bodyforce values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
-  printfluid values = N = print the fluid density and velocity at each grid point every N timesteps. 
-
      - -
    -

    Examples: -

    -
    fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1
-fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873 
-
    -

    Description: -

    -

    Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS -simulation domain. The MD particles described by group-ID apply a velocity -dependent force to the fluid. -

    -

    The lattice-Boltzmann algorithm solves for the fluid motion governed by -the Navier Stokes equations, -

    -
    -
    -

    with, -

    -
    -
    -

    where rho is the fluid density, u is the local fluid velocity, sigma -is the stress tensor, F is a local external force, and eta and Lambda -are the shear and bulk viscosities respectively. Here, we have -implemented -

    -
    -
    -

    with a_0 set to 1/3 (dx/dt)^2 by default. -

    -

    The algorithm involves tracking the time evolution of a set of partial -distribution functions which evolve according to a velocity -discretized version of the Boltzmann equation, -

    -
    -
    -

    where the first term on the right hand side represents a single time -relaxation towards the equilibrium distribution function, and tau is a -parameter physically related to the viscosity. On a technical note, -we have implemented a 15 velocity model (D3Q15) as default; however, -the user can switch to a 19 velocity model (D3Q19) through the use of -the D3Q19 keyword. This fix provides the user with the choice of -two algorithms to solve this equation, through the specification of -the keyword LBtype. If LBtype is set equal to 1, the standard -finite difference LB integrator is used. If LBtype is set equal to -2, the algorithm of Ollila et al. is used. -

    -

    Physical variables are then defined in terms of moments of the distribution -functions, -

    -
    -
    -

    Full details of the lattice-Boltzmann algorithm used can be found in -Mackay et al.. -

    -

    The fluid is coupled to the MD particles described by group-ID -through a velocity dependent force. The contribution to the fluid -force on a given lattice mesh site j due to MD particle alpha is -calculated as: -

    -
    -
    -

    where v_n is the velocity of the MD particle, u_f is the fluid -velocity interpolated to the particle location, and gamma is the force -coupling constant. Zeta is a weight assigned to the grid point, -obtained by distributing the particle to the nearest lattice sites. -For this, the user has the choice between a trilinear stencil, which -provides a support of 8 lattice sites, or the immersed boundary method -Peskin stencil, which provides a support of 64 lattice sites. While -the Peskin stencil is seen to provide more stable results, the -trilinear stencil may be better suited for simulation of objects close -to walls, due to its smaller support. Therefore, by default, the -Peskin stencil is used; however the user may switch to the trilinear -stencil by specifying the keyword, trilinear. -

    -

    By default, the force coupling constant, gamma, is calculated according to -

    -
    -
    -

    Here, m_v is the mass of the MD particle, m_u is a representative -fluid mass at the particle location, and dt_collision is a collision -time, chosen such that tau/dt_collision = 1 (see Mackay and -Denniston for full details). In order to calculate m_u, the -fluid density is interpolated to the MD particle location, and -multiplied by a volume, node_area*dx_lb, where node_area represents -the portion of the surface area of the composite object associated -with a given MD particle. By default, node_area is set equal to -dx_lb*dx_lb; however specific values for given atom types can be set -using the setArea keyword. -

    -

    The user also has the option of specifying their own value for the -force coupling constant, for all the MD particles associated with the -fix, through the use of the setGamma keyword. This may be useful -when modelling porous particles. See Mackay et al. for a -detailed description of the method by which the user can choose an -appropriate gamma value. -

    -

    IMPORTANT NOTE: while this fix applies the force of the particles on -the fluid, it does not apply the force of the fluid to the particles. -When the force coupling constant is set using the default method, -there is only one option to include this hydrodynamic force on the -particles, and that is through the use of the -lb/viscous fix. This fix adds the hydrodynamic -force to the total force acting on the particles, after which any of -the built-in LAMMPS integrators can be used to integrate the particle -motion. However, if the user specifies their own value for the force -coupling constant, as mentioned in Mackay et al., the -built-in LAMMPS integrators may prove to be unstable. Therefore, we -have included our own integrators fix -lb/rigid/pc/sphere, and fix -lb/pc, to solve for the particle motion in these -cases. These integrators should not be used with the -lb/viscous fix, as they add hydrodynamic forces -to the particles directly. In addition, they can not be used if the -force coupling constant has been set the default way. -

    -

    IMPORTANT NOTE: if the force coupling constant is set using the -default method, and the lb/viscous fix is NOT -used to add the hydrodynamic force to the total force acting on the -particles, this physically corresponds to a situation in which an -infinitely massive particle is moving through the fluid (since -collisions between the particle and the fluid do not act to change the -particle's velocity). Therefore, the user should set the mass of the -particle to be significantly larger than the mass of the fluid at the -particle location, in order to approximate an infinitely massive -particle (see the dragforce test run for an example). -

    -
    - -

    Inside the fix, parameters are scaled by the lattice-Boltzmann -timestep, dt, grid spacing, dx, and mass unit, dm. dt is set equal to -(nevery*dt_MD), where dt_MD is the MD timestep. By default, dm is set -equal to 1.0, and dx is chosen so that tau/(dt) = -(3*eta*dt)/(rho*dx^2) is approximately equal to 1. However, the user -has the option of specifying their own values for dm, and dx, by using -the optional keywords dm, and dx respectively. -

    -

    IMPORTANT NOTE: Care must be taken when choosing both a value for dx, -and a simulation domain size. This fix uses the same subdivision of -the simulation domain among processors as the main LAMMPS program. In -order to uniformly cover the simulation domain with lattice sites, the -lengths of the individual LAMMPS subdomains must all be evenly -divisible by dx. If the simulation domain size is cubic, with equal -lengths in all dimensions, and the default value for dx is used, this -will automatically be satisfied. -

    -

    Physical parameters describing the fluid are specified through -viscosity, density, and a0. If the force coupling constant is -set the default way, the surface area associated with the MD particles -is specified using the setArea keyword. If the user chooses to -specify a value for the force coupling constant, this is set using the -setGamma keyword. These parameters should all be given in terms of -the mass, distance, and time units chosen for the main LAMMPS run, as -they are scaled by the LB timestep, lattice spacing, and mass unit, -inside the fix. -

    -
    - -

    The setArea keyword allows the user to associate a surface area with -a given atom type. For example if a spherical composite object of -radius R is represented as a spherical shell of N evenly distributed -MD particles, all of the same type, the surface area per particle -associated with that atom type should be set equal to 4*pi*R^2/N. -This keyword should only be used if the force coupling constant, -gamma, is set the default way. -

    -

    The setGamma keyword allows the user to specify their own value for -the force coupling constant, gamma, instead of using the default -value. -

    -

    The scaleGamma keyword should be used in conjunction with the -setGamma keyword, when the user wishes to specify different gamma -values for different atom types. This keyword allows the user to -scale the setGamma gamma value by a factor, gammaFactor, for a given -atom type. -

    -

    The dx keyword allows the user to specify a value for the LB grid -spacing. -

    -

    The dm keyword allows the user to specify the LB mass unit. -

    -

    If the a0 keyword is used, the value specified is used for the -square of the speed of sound in the fluid. If this keyword is not -present, the speed of sound squared is set equal to (1/3)*(dx/dt)^2. -Setting a0 > (dx/dt)^2 is not allowed, as this may lead to -instabilities. -

    -

    If the noise keyword is used, followed by a a positive temperature -value, and a positive integer random number seed, a thermal -lattice-Boltzmann algorithm is used. If LBtype is set equal to 1 -(i.e. the standard LB integrator is chosen), the thermal LB algorithm -of Adhikari et al. is used; however if LBtype is set -equal to 2 both the LB integrator, and thermal LB algorithm described -in Ollila et al. are used. -

    -

    If the calcforce keyword is used, both the fluid force and torque -acting on the specified particle group are printed to the screen every -N timesteps. -

    -

    If the keyword trilinear is used, the trilinear stencil is used to -interpolate the particle nodes onto the fluid mesh. By default, the -immersed boundary method, Peskin stencil is used. Both of these -interpolation methods are described in Mackay et al.. -

    -

    If the keyword D3Q19 is used, the 19 velocity (D3Q19) lattice is -used by the lattice-Boltzmann algorithm. By default, the 15 velocity -(D3Q15) lattice is used. -

    -

    If the keyword write_restart is used, followed by a positive -integer, N, a binary restart file is printed every N LB timesteps. -This restart file only contains information about the fluid. -Therefore, a LAMMPS restart file should also be written in order to -print out full details of the simulation. -

    -

    IMPORTANT NOTE: When a large number of lattice grid points are used, -the restart files may become quite large. -

    -

    In order to restart the fluid portion of the simulation, the keyword -read_restart is specified, followed by the name of the binary -lb_fluid restart file to be used. -

    -

    If the zwall_velocity keyword is used y-velocities are assigned to -the lower and upper walls. This keyword requires the presence of -walls in the z-direction. This is set by assigning fixed boundary -conditions in the z-direction. If fixed boundary conditions are -present in the z-direction, and this keyword is not used, the walls -are assumed to be stationary. -

    -

    If the bodyforce keyword is used, a constant body force is added to -the fluid, defined by it's x, y and z components. -

    -

    If the printfluid keyword is used, followed by a positive integer, N, -the fluid densities and velocities at each lattice site are printed to the -screen every N timesteps. -

    -
    - -

    For further details, as well as descriptions and results of several -test runs, see Mackay et al.. Please include a citation to -this paper if the lb_fluid fix is used in work contributing to -published research. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Due to the large size of the fluid data, this fix writes it's own -binary restart files, if requested, independent of the main LAMMPS -binary restart files; no information about lb_fluid -is written to the main LAMMPS binary restart files. -

    -

    None of the fix_modify options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various output commands. No -parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix can only be used with an orthogonal simulation domain. -

    -

    Walls have only been implemented in the z-direction. Therefore, the -boundary conditions, as specified via the main LAMMPS boundary command -must be periodic for x and y, and either fixed or periodic for z. -Shrink-wrapped boundary conditions are not permitted with this fix. -

    -

    This fix must be used before any of fix -lb/viscous, fix -lb/momentum, fix -lb/rigid/pc/sphere, and/ or fix -lb/pc , as the fluid needs to be initialized before -any of these routines try to access its properties. In addition, in -order for the hydrodynamic forces to be added to the particles, this -fix must be used in conjunction with the -lb/viscous fix if the force coupling constant is -set by default, or either the lb/viscous fix or -one of the lb/rigid/pc/sphere or -lb/pc integrators, if the user chooses to specifiy -their own value for the force coupling constant. -

    -

    Related commands: -

    -

    fix lb/viscous, fix -lb/momentum, fix -lb/rigid/pc/sphere, fix -lb/pc -

    -

    Default: -

    -

    By default, the force coupling constant is set according to -

    -
    -
    -

    and an area of dx_lb^2 per node, used to calculate the fluid mass at -the particle node location, is assumed. -

    -

    dx is chosen such that tau/(delta t_LB) = -(3 eta dt_LB)/(rho dx_lb^2) is approximately equal to 1. -dm is set equal to 1.0. -a0 is set equal to (1/3)*(dx_lb/dt_lb)^2. -The Peskin stencil is used as the default interpolation method. -The D3Q15 lattice is used for the lattice-Boltzmann algorithm. -If walls are present, they are assumed to be stationary. -

    -
    - - - -

    (Ollila et al.) Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902. -

    - - -

    (Mackay et al.) Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. -

    - - -

    (Mackay and Denniston) Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298. -

    - - -

    (Adhikari et al.) Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479. -

    - diff --git a/doc/doc2/fix_lb_momentum.html b/doc/doc2/fix_lb_momentum.html deleted file mode 100644 index 7092c4e010..0000000000 --- a/doc/doc2/fix_lb_momentum.html +++ /dev/null @@ -1,84 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix lb/momentum command -

    -

    Syntax: -

    -
    fix ID group-ID lb/momentum nevery keyword values ... 
-
    -
    • ID, group-ID are documented in the fix command - -
    • lb/momentum = style name of this fix command - -
    • nevery = adjust the momentum every this many timesteps - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = linear - -
        linear values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include each dimension. 
-
      - -
    -

    Examples: -

    -
    fix 1 sphere lb/momentum 
-fix 1 all lb/momentum linear 1 1 0 
-
    -

    Description: -

    -

    This fix is based on the fix momentum command, and -was created to be used in place of that command, when a -lattice-Boltzmann fluid is present. -

    -

    Zero the total linear momentum of the system, including both the atoms -specified by group-ID and the lattice-Boltzmann fluid every nevery -timesteps. This is accomplished by adjusting the particle velocities -and the fluid velocities at each lattice site. -

    -

    NOTE: This fix only considers the linear momentum of the system. -

    -

    By default, the subtraction is performed for each dimension. This can -be changed by specifying the keyword linear, along with a set of -three flags set to 0/1 in order to exclude/ include the corresponding -dimension. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    Can only be used if a lattice-Boltzmann fluid has been created via the -fix lb/fluid command, and must come after this -command. -

    -

    This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix momentum, fix lb/fluid -

    -

    Default: -

    -

    Zeros the total system linear momentum in each dimension. -

    - diff --git a/doc/doc2/fix_lb_pc.html b/doc/doc2/fix_lb_pc.html deleted file mode 100644 index 8fc22cf84c..0000000000 --- a/doc/doc2/fix_lb_pc.html +++ /dev/null @@ -1,68 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix lb/pc command -

    -

    Syntax: -

    -
    fix ID group-ID lb/pc 
-
    -
    • ID, group-ID are documented in the fix command -
    • lb/pc = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all lb/pc 
-
    -

    Description: -

    -

    Update the positions and velocities of the individual particles -described by group-ID, experiencing velocity-dependent hydrodynamic -forces, using the integration algorithm described in Mackay et -al.. This integration algorithm should only be used if a -user-specified value for the force-coupling constant used in fix -lb/fluid has been set; do not use this integration -algorithm if the force coupling constant has been set by default. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Can only be used if a lattice-Boltzmann fluid has been created via the -fix lb/fluid command, and must come after this -command. -

    -

    Related commands: -

    -

    fix lb/fluid fix -lb/rigid/pc/sphere -

    -

    Default: None. -

    -
    - - - -

    (Mackay et al.) Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. -

    - diff --git a/doc/doc2/fix_lb_rigid_pc_sphere.html b/doc/doc2/fix_lb_rigid_pc_sphere.html deleted file mode 100644 index 0debaa69d6..0000000000 --- a/doc/doc2/fix_lb_rigid_pc_sphere.html +++ /dev/null @@ -1,158 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix lb/rigid/pc/sphere command -

    -

    Syntax: -

    -
    fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • lb/rigid/pc/sphere = style name of this fix command - -
    • bodystyle = single or molecule or group - -
    • single args = none - molecule args = none - group args = N groupID1 groupID2 ... - N = # of groups -zero or more keyword/value pairs may be appended - -
    • keyword = force or torque or innerNodes - -
        force values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass force is active
-  torque values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass torque is active 
-  innerNodes values = innergroup-ID 
-    innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid 
-
      - -
    -

    Examples: -

    -
    fix 1 spheres lb/rigid/pc/sphere 
-fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms 
-
    -

    Description: -

    -

    This fix is based on the fix rigid command, and was -created to be used in place of that fix, to integrate the equations of -motion of spherical rigid bodies when a lattice-Boltzmann fluid is -present with a user-specified value of the force-coupling constant. -The fix uses the integration algorithm described in Mackay et -al. to update the positions, velocities, and orientations of -a set of spherical rigid bodies experiencing velocity dependent -hydrodynamic forces. The spherical bodies are assumed to rotate as -solid, uniform density spheres, with moments of inertia calculated -using the combined sum of the masses of all the constituent particles -(which are assumed to be point particles). -

    -
    - -

    By default, all of the atoms that this fix acts on experience a -hydrodynamic force due to the presence of the lattice-Boltzmann fluid. -However, the innerNodes keyword allows the user to specify atoms -belonging to a rigid object which do not interact with the -lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic -force from the lattice-Boltzmann fluid). This can be used to -distinguish between atoms on the surface of a non-porous object, and -those on the inside. -

    -

    This feature can be used, for example, when implementing a hard sphere -interaction between two spherical objects. Instead of interactions -occurring between the particles on the surfaces of the two spheres, it -is desirable simply to place an atom at the center of each sphere, -which does not contribute to the hydrodynamic force, and have these -central atoms interact with one another. -

    -
    - -

    Apart from the features described above, this fix is very similar to -the rigid fix (although it includes fewer optional arguments, and -assumes the constituent atoms are point particles); see -fix_rigid for a complete documentation. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about the rigid and rigid/nve fixes are written to -binary restart files. -

    -

    Similar to the fix_rigid command: " The rigid -fix computes a global scalar which can be accessed by various output -commands. The scalar value calculated by -these fixes is "intensive". The scalar is the current temperature of -the collection of rigid bodies. This is averaged over all rigid -bodies and their translational and rotational degrees of freedom. The -translational energy of a rigid body is 1/2 m v^2, where m = total -mass of the body and v = the velocity of its center of mass. The -rotational energy of a rigid body is 1/2 I w^2, where I = the moment -of inertia tensor of the body and w = its angular velocity. Degrees -of freedom constrained by the force and torque keywords are -removed from this calculation." -

    -

    "All of these fixes compute a global array of values which can be -accessed by various output commands. -The number of rows in the array is equal to the number of rigid -bodies. The number of columns is 15. Thus for each rigid body, 15 -values are stored: the xyz coords of the center of mass (COM), the xyz -components of the COM velocity, the xyz components of the force acting -on the COM, the xyz components of the torque acting on the COM, and -the xyz image flags of the COM, which have the same meaning as image -flags for atom positions (see the "dump" command). The force and -torque values in the array are not affected by the force and -torque keywords in the fix rigid command; they reflect values before -any changes are made by those keywords. -

    -

    The ordering of the rigid bodies (by row in the array) is as follows. -For the single keyword there is just one rigid body. For the -molecule keyword, the bodies are ordered by ascending molecule ID. -For the group keyword, the list of group IDs determines the ordering -of bodies. -

    -

    The array values calculated by these fixes are "intensive", meaning -they are independent of the number of atoms in the simulation. -

    -

    No parameter of these fixes can be used with the start/stop keywords -of the run command. These fixes are not invoked during -energy minimization. " -

    -

    Restrictions: -

    -

    This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Can only be used if a lattice-Boltzmann fluid has been created via the -fix lb/fluid command, and must come after this -command. Should only be used if the force coupling constant used in -fix lb/fluid has been set by the user; this -integration fix cannot be used if the force coupling constant is set -by default. -

    -

    Related commands: -

    -

    fix lb/fluid, fix lb/pc -

    -

    Default: -

    -

    The defaults are force * on on on, and torque * on on on. -

    -
    - - - -

    (Mackay et al.) Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. -

    - diff --git a/doc/doc2/fix_lb_viscous.html b/doc/doc2/fix_lb_viscous.html deleted file mode 100644 index d9c87884b9..0000000000 --- a/doc/doc2/fix_lb_viscous.html +++ /dev/null @@ -1,100 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix lb/viscous command -

    -

    Syntax: -

    -
    fix ID group-ID lb/viscous 
-
    -
    • ID, group-ID are documented in fix command -
    • lb/viscous = style name of this fix command -
    -

    Examples: -

    -

    fix 1 flow lb/viscous -

    -

    Description: -

    -

    This fix is similar to the fix viscous command, and -is to be used in place of that command when a lattice-Boltzmann fluid -is present, and the user wishes to integrate the particle motion using -one of the built in LAMMPS integrators. -

    -

    This fix adds a force, F = - Gamma*(velocity-fluid_velocity), to each -atom, where Gamma is the force coupling constant described in the fix -lb/fluid command (which applies an equal and -opposite force to the fluid). -

    -

    IMPORTANT NOTE: This fix should only be used in conjunction with one -of the built in LAMMPS integrators; it should not be used with the -fix lb/pc or fix -lb/rigid/pc/sphere integrators, which -already include the hydrodynamic forces. These latter fixes should -only be used if the force coupling constant has been set by the user -(instead of using the default value); if the default force coupling -value is used, then this fix provides the only method for adding the -hydrodynamic forces to the particles. -

    -
    - -

    For further details, as well as descriptions and results of several -test runs, see Mackay et al.. Please include a citation to -this paper if this fix is used in work contributing to published -research. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    As described in the fix viscous documentation: -

    -

    "No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. This fix should only -be used with damped dynamics minimizers that allow for -non-conservative forces. See the min_style command -for details." -

    -

    Restrictions: -

    -

    This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Can only be used if a lattice-Boltzmann fluid has been created via the -fix lb/fluid command, and must come after this -command. -

    -

    This fix should not be used if either the fix lb/pc -or fix lb/rigid/pc/sphere integrator is -used. -

    -

    Related commands: -

    -

    fix lb/fluid, fix lb/pc, fix -lb/rigid/pc/sphere -

    -

    Default: none -

    -
    - - - -

    (Mackay et al.) Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. -

    - diff --git a/doc/doc2/fix_lineforce.html b/doc/doc2/fix_lineforce.html deleted file mode 100644 index 9c87f094e2..0000000000 --- a/doc/doc2/fix_lineforce.html +++ /dev/null @@ -1,56 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix lineforce command -

    -

    Syntax: -

    -
    fix ID group-ID lineforce x y z 
-
    -
    • ID, group-ID are documented in fix command -
    • lineforce = style name of this fix command -
    • x y z = direction of line as a 3-vector -
    -

    Examples: -

    -
    fix hold boundary lineforce 0.0 1.0 1.0 
-
    -

    Description: -

    -

    Adjust the forces on each atom in the group so that only the component -of force along the linear direction specified by the vector (x,y,z) -remains. This is done by subtracting out components of force in the -plane perpendicular to the line. -

    -

    If the initial velocity of the atom is 0.0 (or along the line), then -it should continue to move along the line thereafter. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix planeforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_meso.html b/doc/doc2/fix_meso.html deleted file mode 100644 index 81bb833347..0000000000 --- a/doc/doc2/fix_meso.html +++ /dev/null @@ -1,57 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix meso command -

    -

    Syntax: -

    -
    fix ID group-ID meso 
-
    -
    • ID, group-ID are documented in fix command -
    • meso = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all meso 
-
    -

    Description: -

    -

    Perform time integration to update position, velocity, internal energy -and local density for atoms in the group each timestep. This fix is -needed to time-integrate mesoscopic systems where particles carry -internal variables such as SPH or DPDE. -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    "fix meso/stationary" -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_meso_stationary.html b/doc/doc2/fix_meso_stationary.html deleted file mode 100644 index cf339c2560..0000000000 --- a/doc/doc2/fix_meso_stationary.html +++ /dev/null @@ -1,58 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix meso/stationary command -

    -

    Syntax: -

    -
    fix ID group-ID meso/stationary 
-
    -
    • ID, group-ID are documented in fix command -
    • meso = style name of this fix command -
    -

    Examples: -

    -
    fix 1 boundary meso/stationary 
-
    -

    Description: -

    -

    Perform time integration to update internal energy and local density, -but not position or velocity for atoms in the group each timestep. -This fix is needed for SPH simulations to correctly time-integrate -fixed boundary particles which constrain a fluid to a given region in -space. -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    "fix meso" -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_modify.html b/doc/doc2/fix_modify.html deleted file mode 100644 index d31aada56e..0000000000 --- a/doc/doc2/fix_modify.html +++ /dev/null @@ -1,81 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix_modify command -

    -

    Syntax: -

    -
    fix_modify fix-ID keyword value ... 
-
    -
    • fix-ID = ID of the fix to modify - -
    • one or more keyword/value pairs may be appended - -
    • keyword = temp or press or energy - -
        temp value = compute ID that calculates a temperature
-  press value = compute ID that calculates a pressure
-  energy value = yes or no 
-
      - -
    -

    Examples: -

    -
    fix_modify 3 temp myTemp press myPress
-fix_modify 1 energy yes 
-
    -

    Description: -

    -

    Modify one or more parameters of a previously defined fix. Only -specific fix styles support specific parameters. See the doc pages -for individual fix commands for info on which ones support which -fix_modify parameters. -

    -

    The temp keyword is used to determine how a fix computes -temperature. The specified compute ID must have been previously -defined by the user via the compute command and it must -be a style of compute that calculates a temperature. All fixes that -compute temperatures define their own compute by default, as described -in their documentation. Thus this option allows the user to override -the default method for computing T. -

    -

    The press keyword is used to determine how a fix computes pressure. -The specified compute ID must have been previously defined by the user -via the compute command and it must be a style of -compute that calculates a pressure. All fixes that compute pressures -define their own compute by default, as described in their -documentation. Thus this option allows the user to override the -default method for computing P. -

    -

    For fixes that calculate a contribution to the potential energy of the -system, the energy keyword will include that contribution in -thermodynamic output of potential energy. See the -thermo_style command for info on how potential -energy is output. The contribution by itself can be printed by using -the keyword f_ID in the thermo_style custom command, where ID is the -fix-ID of the appropriate fix. Note that you must use this setting -for a fix if you are using it when performing an energy -minimization and if you want the energy and forces it -produces to be part of the optimization criteria. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix, compute temp, compute -pressure, thermo_style -

    -

    Default: -

    -

    The option defaults are temp = ID defined by fix, press = ID defined -by fix, energy = no. -

    - diff --git a/doc/doc2/fix_momentum.html b/doc/doc2/fix_momentum.html deleted file mode 100644 index c17c44a3fc..0000000000 --- a/doc/doc2/fix_momentum.html +++ /dev/null @@ -1,85 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix momentum command -

    -

    Syntax: -

    -
    fix ID group-ID momentum N keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • momentum = style name of this fix command - -
    • N = adjust the momentum every this many timesteps -one or more keyword/value pairs may be appended - -
    • keyword = linear or angular or rescale - -
        linear values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include each dimension
-  angular values = none 
-
      -
        rescale values = none 
-
      - -
    -

    Examples: -

    -
    fix 1 all momentum 1 linear 1 1 0
-fix 1 all momentum 1 linear 1 1 1 rescale
-fix 1 all momentum 100 linear 1 1 1 angular 
-
    -

    Description: -

    -

    Zero the linear and/or angular momentum of the group of atoms every N -timesteps by adjusting the velocities of the atoms. One (or both) of -the linear or angular keywords must be specified. -

    -

    If the linear keyword is used, the linear momentum is zeroed by -subtracting the center-of-mass velocity of the group from each atom. -This does not change the relative velocity of any pair of atoms. One -or more dimensions can be excluded from this operation by setting the -corresponding flag to 0. -

    -

    If the angular keyword is used, the angular momentum is zeroed by -subtracting a rotational component from each atom. -

    -

    This command can be used to insure the entire collection of atoms (or -a subset of them) does not drift or rotate during the simulation due -to random perturbations (e.g. fix langevin -thermostatting). -

    -

    The rescale keyword enables conserving the kinetic energy of the group -of atoms by rescaling the velocities after the momentum was removed. -

    -

    Note that the velocity command can be used to create -initial velocities with zero aggregate linear and/or angular momentum. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix recenter, velocity -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_move.html b/doc/doc2/fix_move.html deleted file mode 100644 index 099f269c8d..0000000000 --- a/doc/doc2/fix_move.html +++ /dev/null @@ -1,234 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix move command -

    -

    Syntax: -

    -
    fix ID group-ID move style args keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • move = style name of this fix command - -
    • style = linear or wiggle or rotate or variable - -
        linear args = Vx Vy Vz
-    Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
-  wiggle args = Ax Ay Az period
-    Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
-    period = period of oscillation (time units)
-  rotate args = Px Py Pz Rx Ry Rz period
-    Px,Py,Pz = origin point of axis of rotation (distance units)
-    Rx,Ry,Rz = axis of rotation vector
-    period = period of rotation (time units)
-  variable args = v_dx v_dy v_dz v_vx v_vy v_vz
-    v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
-    v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = units - -
        units value = box or lattice 
-
      - -
    -

    Examples: -

    -
    fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
-fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
-fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL 
-
    -

    Description: -

    -

    Perform updates of position and velocity for atoms in the group each -timestep using the specified settings or formulas, without regard to -forces on the atoms. This can be useful for boundary or other atoms, -whose movement can influence nearby atoms. -

    -

    IMPORTANT NOTE: The atoms affected by this fix should not normally be -time integrated by other fixes (e.g. fix nve, fix -nvt), since that will change their positions and -velocities twice. -

    -

    IMPORTANT NOTE: As atoms move due to this fix, they will pass thru -periodic boundaries and be remapped to the other side of the -simulation box, just as they would during normal time integration -(e.g. via the fix nve command). It is up to you to -decide whether periodic boundaries are appropriate with the kind of -atom motion you are prescribing with this fix. -

    -

    IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their -initial position at the time the fix is specified. These initial -coordinates are stored by the fix in "unwrapped" form, by using the -image flags associated with each atom. See the dump -custom command for a discussion of "unwrapped" coordinates. -See the Atoms section of the read_data command for a -discussion of image flags and how they are set for each atom. You can -reset the image flags (e.g. to 0) before invoking this fix by using -the set image command. -

    -
    - -

    The linear style moves atoms at a constant velocity, so that their -position X = (x,y,z) as a function of time is given in vector -notation as -

    -
    X(t) = X0 + V * delta 
-
    -

    where X0 = (x0,y0,z0) is their position at the time the fix is -specified, V is the specified velocity vector with components -(Vx,Vy,Vz), and delta is the time elapsed since the fix was -specified. This style also sets the velocity of each atom to V = -(Vx,Vy,Vz). If any of the velocity components is specified as NULL, -then the position and velocity of that component is time integrated -the same as the fix nve command would perform, using -the corresponding force component on the atom. -

    -

    Note that the linear style is identical to using the variable -style with an equal-style variable that uses the -vdisplace() function. E.g. -

    -
    variable V equal 10.0
-variable x equal vdisplace(0.0,$V)
-fix 1 boundary move variable v_x NULL NULL v_V NULL NULL 
-
    -

    The wiggle style moves atoms in an oscillatory fashion, so that -their position X = (x,y,z) as a function of time is given in vector -notation as -

    -
    X(t) = X0 + A sin(omega*delta) 
-
    -

    where X0 = (x0,y0,z0) is their position at the time the fix is -specified, A is the specified amplitude vector with components -(Ax,Ay,Az), omega is 2 PI / period, and delta is the time -elapsed since the fix was specified. This style also sets the -velocity of each atom to the time derivative of this expression. If -any of the amplitude components is specified as NULL, then the -position and velocity of that component is time integrated the same as -the fix nve command would perform, using the -corresponding force component on the atom. -

    -

    Note that the wiggle style is identical to using the variable -style with equal-style variables that use the -swiggle() and cwiggle() functions. E.g. -

    -
    variable A equal 10.0
-variable T equal 5.0
-variable omega equal 2.0*PI/$T
-variable x equal swiggle(0.0,$A,$T)
-variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
-fix 1 boundary move variable v_x NULL NULL v_v NULL NULL 
-
    -

    The rotate style rotates atoms around a rotation axis R = -(Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz). The period of -the rotation is also specified. This style also sets the velocity of -each atom to (omega cross Rperp) where omega is its angular velocity -around the rotation axis and Rperp is a perpendicular vector from the -rotation axis to the atom. If the defined -atom_style assigns an angular velocity to each atom, -then each atom's angular velocity is also set to omega. Note that the -direction of rotation for the atoms around the rotation axis is -consistent with the right-hand rule: if your right-hand's thumb points -along R, then your fingers wrap around the axis in the direction of -rotation. -

    -

    The variable style allows the position and velocity components of -each atom to be set by formulas specified via the -variable command. Each of the 6 variables is -specified as an argument to the fix as v_name, where name is the -variable name that is defined elsewhere in the input script. -

    -

    Each variable must be of either the equal or atom style. -Equal-style variables compute a single numeric quantity, that can be -a function of the timestep as well as of other simulation values. -Atom-style variables compute a numeric quantity for each atom, that -can be a function per-atom quantities, such as the atom's position, as -well as of the timestep and other simulation values. Note that this -fix stores the original coordinates of each atom (see note below) so -that per-atom quantity can be used in an atom-style variable formula. -See the variable command for details. -

    -

    The first 3 variables (v_dx,v_dy,v_dz) specified for the variable -style are used to calculate a displacement from the atom's original -position at the time the fix was specified. The second 3 variables -(v_vx,v_vy,v_vz) specified are used to compute a velocity for each -atom. -

    -

    Any of the 6 variables can be specified as NULL. If both the -displacement and velocity variables for a particular x,y,z component -are specified as NULL, then the position and velocity of that -component is time integrated the same as the fix nve -command would perform, using the corresponding force component on the -atom. If only the velocity variable for a component is specified as -NULL, then the displacement variable will be used to set the position -of the atom, and its velocity component will not be changed. If only -the displacement variable for a component is specified as NULL, then -the velocity variable will be used to set the velocity of the atom, -and the position of the atom will be time integrated using that -velocity. -

    -

    The units keyword determines the meaning of the distance units used -to define the linear velocity and wiggle amplitude and rotate -origin. This setting is ignored for the variable style. A box -value selects standard units as defined by the units -command, e.g. velocity in Angstroms/fmsec and amplitude and position -in Angstroms for units = real. A lattice value means the velocity -units are in lattice spacings per time and the amplitude and position -are in lattice spacings. The lattice command must have -been previously used to define the lattice spacing. Each of these 3 -quantities may be dependent on the x,y,z dimension, since the lattice -spacings can be different in x,y,z. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the original coordinates of moving atoms to binary -restart files, as well as the initial timestep, so that -the motion can be continuous in a restarted simulation. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    IMPORTANNT NOTE: Because the move positions are a function of the -current timestep and the initial timestep, you cannot reset the -timestep to a different value after reading a restart file, if you -expect a fix move command to work in an uninterrupted fashion. -

    -

    None of the fix_modify options are relevant to this -fix. -

    -

    This fix produces a per-atom array which can be accessed by various -output commands. The number of columns -for each atom is 3, and the columns store the original unwrapped x,y,z -coords of each atom. The per-atom values can be accessed on any -timestep. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    For rRESPA time integration, this fix adjusts the -position and velocity of atoms on the outermost rRESPA level. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix nve, displace_atoms -

    -

    Default: none -

    -

    The option default is units = lattice. -

    - diff --git a/doc/doc2/fix_msst.html b/doc/doc2/fix_msst.html deleted file mode 100644 index 60f2daffe7..0000000000 --- a/doc/doc2/fix_msst.html +++ /dev/null @@ -1,171 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix msst command -

    -

    Syntax: -

    -
    fix ID group-ID msst dir shockvel keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • msst = style name of this fix - -
    • dir = x or y or z - -
    • shockvel = shock velocity (strictly positive, distance/time units) - -
    • zero or more keyword value pairs may be appended - -
    • keyword = q or mu or p0 or v0 or e0 or tscale - -
        q value = cell mass-like parameter (mass^2/distance^4 units)
-  mu value = artificial viscosity (mass/length/time units)
-  p0 value = initial pressure in the shock equations (pressure units)
-  v0 value = initial simulation cell volume in the shock equations (distance^3 units)  
-  e0 value = initial total energy (energy units)
-  tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) 
-
      - -
    -

    Examples: -

    -
    fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
-fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4  v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 
-
    -

    Description: -

    -

    This command performs the Multi-Scale Shock Technique (MSST) -integration to update positions and velocities each timestep to mimic -a compressive shock wave passing over the system. See (Reed) -for a detailed description of this method. The MSST varies the cell -volume and temperature in such a way as to restrain the system to the -shock Hugoniot and the Rayleigh line. These restraints correspond to -the macroscopic conservation laws dictated by a shock -front. shockvel determines the steady shock velocity that will be -simulated. -

    -

    To perform a simulation, choose a value of q that provides volume -compression on the timescale of 100 fs to 1 ps. If the volume is not -compressing, either the shock speed is chosen to be below the material -sound speed or p0 has been chosen inaccurately. Volume compression -at the start can be sped up by using a non-zero value of tscale. Use -the smallest value of tscale that results in compression. -

    -

    Under some special high-symmetry conditions, the pressure (volume) -and/or temperature of the system may oscillate for many cycles even -with an appropriate choice of mass-like parameter q. Such -oscillations have physical significance in some cases. The optional -mu keyword adds an artificial viscosity that helps break the system -symmetry to equilibrate to the shock Hugoniot and Rayleigh line more -rapidly in such cases. -

    -

    tscale is a factor between 0 and 1 that determines what fraction of -thermal kinetic energy is converted to compressive strain kinetic -energy at the start of the simulation. Setting this parameter to a -non-zero value may assist in compression at the start of simulations -where it is slow to occur. -

    -

    If keywords e0, p0,or v0 are not supplied, these quantities will -be calculated on the first step, after the energy specified by -tscale is removed. The value of e0 is not used in the dynamical -equations, but is used in calculating the deviation from the Hugoniot. -

    -

    Values of shockvel less than a critical value determined by the -material response will not have compressive solutions. This will be -reflected in lack of significant change of the volume in the MSST. -

    -

    For all pressure styles, the simulation box stays orthogonal in shape. -Parrinello-Rahman boundary conditions (tilted box) are supported by -LAMMPS, but are not implemented for MSST. -

    -

    This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if these commands had been issued: -

    -
    compute fix-ID_temp group-ID temp 
-compute fix-ID_press group-ID pressure fix-ID_temp 
-
    -

    See the compute temp and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press". The group for the new computes is "all". -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of all internal variables to binary restart -files. See the read_restart command -for info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    The progress of the MSST can be monitored by printing the global -scalar and global vector quantities computed by the fix. -

    -

    The scalar is the cumulative energy change due to the fix. This is -also the energy added to the potential energy by the -fix_modify energy command. With this command, the -thermo keyword etotal prints the conserved quantity of the MSST -dynamic equations. This can be used to test if the MD timestep is -sufficiently small for accurate integration of the dynamic -equations. See also thermo_style command. -

    -

    The global vector contains four values in this order: -

    -

    [dhugoniot, drayleigh, lagrangian_speed, lagrangian_position] -

    -
    1. dhugoniot is the departure from the Hugoniot (temperature units). -
    2. drayleigh is the departure from the Rayleigh line (pressure units). -
    3. lagrangian_speed is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). -
    4. lagrangian_position is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front. -
    -

    To print these quantities to the log file with descriptive column -headers, the following LAMMPS commands are suggested: -

    -
    fix		 msst all msst z 
-fix_modify       msst energy yes
-variable dhug    equal f_msst[1]
-variable dray    equal f_msst[2]
-variable lgr_vel equal f_msst[3]
-variable lgr_pos equal f_msst[4]
-thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst 
-
    -

    These fixes compute a global scalar and a global vector of 4 -quantities, which can be accessed by various output -commands. The scalar values calculated -by this fix are "extensive"; the vector values are "intensive". -

    -

    Restrictions: -

    -

    This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    All cell dimensions must be periodic. This fix can not be used with a -triclinic cell. The MSST fix has been tested only for the group-ID -all. -

    -

    Related commands: -

    -

    fix nphug, fix deform -

    -

    Default: -

    -

    The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0 -are calculated on the first step. -

    -
    - - - -

    (Reed) Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003). -

    - diff --git a/doc/doc2/fix_neb.html b/doc/doc2/fix_neb.html deleted file mode 100644 index 23a8b894d3..0000000000 --- a/doc/doc2/fix_neb.html +++ /dev/null @@ -1,113 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix neb command -

    -

    Syntax: -

    -
    fix ID group-ID neb Kspring 
-
    -
    • ID, group-ID are documented in fix command -
    • neb = style name of this fix command -
    • Kspring = inter-replica spring constant (force/distance units) -
    -

    Examples: -

    -
    fix 1 active neb 10.0 
-
    -

    Description: -

    -

    Add inter-replica forces to atoms in the group for a multi-replica -simulation run via the neb command to perform a nudged -elastic band (NEB) calculation for transition state finding. Hi-level -explanations of NEB are given with the neb command and in -Section_howto 5 of the manual. The fix -neb command must be used with the "neb" command to define how -inter-replica forces are computed. -

    -

    Only the N atoms in the fix group experience inter-replica forces. -Atoms in the two end-point replicas do not experience these forces, -but those in intermediate replicas do. During the initial stage of -NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting -on the atoms of each intermediate replica I is altered, as described -in the (Henkelman1) paper, to become: -

    -
    Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That 
-
    -

    Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the -coordinates of its neighbor replicas. That (t with a hat over it) is -the unit "tangent" vector for replica I which is a function of Ri, -Ri-1, Ri+1, and the potential energy of the 3 replicas; it points -roughly in the direction of (Ri+i - Ri-1); see the -(Henkelman1) paper for details. -

    -

    The first two terms in the above equation are the component of the -interatomic forces perpendicular to the tangent vector. The last term -is a spring force between replica I and its neighbors, parallel to the -tangent vector direction with the specified spring constant Kspring. -

    -

    The effect of the first two terms is to push the atoms of each replica -toward the minimum energy path (MEP) of conformational states that -transition over the energy barrier. The MEP for an energy barrier is -defined as a sequence of 3N-dimensional states which cross the barrier -at its saddle point, each of which has a potential energy gradient -parallel to the MEP itself. -

    -

    The effect of the last term is to push each replica away from its two -neighbors in a direction along the MEP, so that the final set of -states are equidistant from each other. -

    -

    During the second stage of NEB, the forces on the N atoms in the -replica nearest the top of the energy barrier are altered so that it -climbs to the top of the barrier and finds the saddle point. The -forces on atoms in this replica are described in the -(Henkelman2) paper, and become: -

    -
    Fi = -Grad(V) + 2 (Grad(V) dot That) That 
-
    -

    The inter-replica forces for the other replicas are unchanged from the -first equation. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -as invoked by the minimize command via the -neb command. -

    -

    Restrictions: -

    -

    This command can only be used if LAMMPS was built with the REPLICA -package. See the Making LAMMPS section -for more info on packages. -

    -

    Related commands: -

    -

    neb -

    -

    Default: none -

    - - -

    (Henkelman1) Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). -

    - - -

    (Henkelman2) Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, -9901-9904 (2000). -

    - diff --git a/doc/doc2/fix_nh.html b/doc/doc2/fix_nh.html deleted file mode 100644 index df6fdd0d4e..0000000000 --- a/doc/doc2/fix_nh.html +++ /dev/null @@ -1,633 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nvt command -

    -

    fix nvt/cuda command -

    -

    fix nvt/kk command -

    -

    fix nvt/omp command -

    -

    fix npt command -

    -

    fix npt/cuda command -

    -

    fix npt/kk command -

    -

    fix npt/omp command -

    -

    fix nph command -

    -

    fix nph/kk command -

    -

    fix nph/omp command -

    -

    Syntax: -

    -
    fix ID group-ID style_name keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • style_name = nvt or npt or nph - -
    • one or more keyword/value pairs may be appended - -
      keyword = temp or iso or aniso or tri or x or y or z or xy or yz or xz or couple or tchain or pchain or mtk or tloop or ploop or nreset or drag or dilate or scalexy or scaleyz or scalexz or flip or fixedpoint
-  temp values = Tstart Tstop Tdamp
-    Tstart,Tstop = external temperature at start/end of run
-    Tdamp = temperature damping parameter (time units)
-  iso or aniso or tri values = Pstart Pstop Pdamp
-    Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
-    Pdamp = pressure damping parameter (time units)
-  x or y or z or xy or yz or xz values = Pstart Pstop Pdamp
-    Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
-    Pdamp = stress damping parameter (time units)
-  couple = none or xyz or xy or yz or xz
-  tchain value = N
-    N = length of thermostat chain (1 = single thermostat)
-  pchain values = N
-    N length of thermostat chain on barostat (0 = no thermostat)
-  mtk value = yes or no = add in MTK adjustment term or not
-  tloop value = M
-    M = number of sub-cycles to perform on thermostat
-  ploop value = M
-    M = number of sub-cycles to perform on barostat thermostat
-  nreset value = reset reference cell every this many timesteps
-  drag value = Df
-    Df = drag factor added to barostat/thermostat (0.0 = no drag)
-  dilate value = dilate-group-ID
-    dilate-group-ID = only dilate atoms in this group due to barostat volume changes
-  scalexy value = yes or no = scale xy with ly
-  scaleyz value = yes or no = scale yz with lz
-  scalexz value = yes or no = scale xz with lz
-  flip value = yes or no = allow or disallow box flips when it becomes highly skewed
-  fixedpoint values = x y z
-    x,y,z = perform barostat dilation/contraction around this point (distance units) 
-
      - -
    -

    Examples: -

    -
    fix 1 all nvt temp 300.0 300.0 100.0
-fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
-fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
-fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 
-
    -

    Description: -

    -

    These commands perform time integration on Nose-Hoover style -non-Hamiltonian equations of motion which are designed to generate -positions and velocities sampled from the canonical (nvt), -isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This -updates the position and velocity for atoms in the group each -timestep. -

    -

    The thermostatting and barostatting is achieved by adding some dynamic -variables which are coupled to the particle velocities -(thermostatting) and simulation domain dimensions (barostatting). In -addition to basic thermostatting and barostatting, these fixes can -also create a chain of thermostats coupled to the particle thermostat, -and another chain of thermostats coupled to the barostat -variables. The barostat can be coupled to the overall box volume, or -to individual dimensions, including the xy, xz and yz tilt -dimensions. The external pressure of the barostat can be specified as -either a scalar pressure (isobaric ensemble) or as components of a -symmetric stress tensor (constant stress ensemble). When used -correctly, the time-averaged temperature and stress tensor of the -particles will match the target values specified by Tstart/Tstop and -Pstart/Pstop. -

    -

    The equations of motion used are those of Shinoda et al in -(Shinoda), which combine the hydrostatic equations of -Martyna, Tobias and Klein in (Martyna) with the strain -energy proposed by Parrinello and Rahman in -(Parrinello). The time integration schemes closely -follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al. in (Tuckerman). -

    -
    - -

    The thermostat parameters for fix styles nvt and npt is specified -using the temp keyword. Other thermostat-related keywords are -tchain, tloop and drag, which are discussed below. -

    -

    The thermostat is applied to only the translational degrees of freedom -for the particles. The translational degrees of freedom can also have -a bias velocity removed before thermostatting takes place; see the -description below. The desired temperature at each timestep is a -ramped value during the run from Tstart to Tstop. The Tdamp -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 10.0 means to relax -the temperature in a timespan of (roughly) 10 time units (e.g. tau or -fmsec or psec - see the units command). The atoms in the -fix group are the only ones whose velocities and positions are updated -by the velocity/position update portion of the integration. -

    -

    IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for -arbitrary values of Tdamp. If Tdamp is too small, the temperature -can fluctuate wildly; if it is too large, the temperature will take a -very long time to equilibrate. A good choice for many models is a -Tdamp of around 100 timesteps. Note that this is NOT the same as -100 time units for most units settings. -

    -
    - -

    The barostat parameters for fix styles npt and nph is specified -using one or more of the iso, aniso, tri, x, y, z, xy, -xz, yz, and couple keywords. These keywords give you the -ability to specify all 6 components of an external stress tensor, and -to couple various of these components together so that the dimensions -they represent are varied together during a constant-pressure -simulation. -

    -

    Other barostat-related keywords are pchain, mtk, ploop, -nreset, drag, and dilate, which are discussed below. -

    -

    Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). -Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The create_box, read -data, and read_restart commands -specify whether the simulation box is orthogonal or non-orthogonal -(triclinic) and explain the meaning of the xy,xz,yz tilt factors. -

    -

    The target pressures for each of the 6 components of the stress tensor -can be specified independently via the x, y, z, xy, xz, yz -keywords, which correspond to the 6 simulation box dimensions. For -each component, the external pressure or tensor component at each -timestep is a ramped value during the run from Pstart to Pstop. -If a target pressure is specified for a component, then the -corresponding box dimension will change during a simulation. For -example, if the y keyword is used, the y-box length will change. If -the xy keyword is used, the xy tilt factor will change. A box -dimension will not change if that component is not specified, although -you have the option to change that dimension via the fix -deform command. -

    -

    Note that in order to use the xy, xz, or yz keywords, the -simulation box must be triclinic, even if its initial tilt factors are -0.0. -

    -

    For all barostat keywords, the Pdamp parameter operates like the -Tdamp parameter, determining the time scale on which pressure is -relaxed. For example, a value of 10.0 means to relax the pressure in -a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see -the units command). -

    -

    IMPORTANT NOTE: A Nose-Hoover barostat will not work well for -arbitrary values of Pdamp. If Pdamp is too small, the pressure -and volume can fluctuate wildly; if it is too large, the pressure will -take a very long time to equilibrate. A good choice for many models -is a Pdamp of around 1000 timesteps. Note that this is NOT the same -as 1000 time units for most units settings. -

    -

    Regardless of what atoms are in the fix group (the only atoms which -are time integrated), a global pressure or stress tensor is computed -for all atoms. Similarly, when the size of the simulation box is -changed, all atoms are re-scaled to new positions, unless the keyword -dilate is specified with a dilate-group-ID for a group that -represents a subset of the atoms. This can be useful, for example, to -leave the coordinates of atoms in a solid substrate unchanged and -controlling the pressure of a surrounding fluid. This option should -be used with care, since it can be unphysical to dilate some atoms and -not others, because it can introduce large, instantaneous -displacements between a pair of atoms (one dilated, one not) that are -far from the dilation origin. Also note that for atoms not in the fix -group, a separate time integration fix like fix nve or -fix nvt can be used on them, independent of whether they -are dilated or not. -

    -
    - -

    The couple keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, xz -means the Pxx and Pzz components of the stress tensor are coupled. -Xyz means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -Pstart, Pstop, Pdamp parameters for any coupled dimensions must -be identical. Couple xyz can be used for a 2d simulation; the z -dimension is simply ignored. -

    -
    - -

    The iso, aniso, and tri keywords are simply shortcuts that are -equivalent to specifying several other keywords together. -

    -

    The keyword iso means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Pstart Pstop Pdamp" is the same as -specifying these 4 keywords: -

    -
    x Pstart Pstop Pdamp
-y Pstart Pstop Pdamp
-z Pstart Pstop Pdamp
-couple xyz 
-
    -

    The keyword aniso means x, y, and z dimensions are controlled -independently using the Pxx, Pyy, and Pzz components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying -these 4 keywords: -

    -
    x Pstart Pstop Pdamp
-y Pstart Pstop Pdamp
-z Pstart Pstop Pdamp
-couple none 
-
    -

    The keyword tri means x, y, z, xy, xz, and yz dimensions -are controlled independently using their individual stress components -as the driving forces, and the specified scalar pressure as the -external normal stress. Using "tri Pstart Pstop Pdamp" is the same as -specifying these 7 keywords: -

    -
    x Pstart Pstop Pdamp
-y Pstart Pstop Pdamp
-z Pstart Pstop Pdamp
-xy 0.0 0.0 Pdamp
-yz 0.0 0.0 Pdamp
-xz 0.0 0.0 Pdamp
-couple none 
-
    -
    - -

    In some cases (e.g. for solids) the pressure (volume) and/or -temperature of the system can oscillate undesirably when a Nose/Hoover -barostat and thermostat is applied. The optional drag keyword will -damp these oscillations, although it alters the Nose/Hoover equations. -A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. -A non-zero value adds a drag term; the larger the value specified, the -greater the damping effect. Performing a short run and monitoring the -pressure and temperature is the best way to determine if the drag term -is working. Typically a value between 0.2 to 2.0 is sufficient to -damp oscillations after a few periods. Note that use of the drag -keyword will interfere with energy conservation and will also change -the distribution of positions and velocities so that they do not -correspond to the nominal NVT, NPT, or NPH ensembles. -

    -

    An alternative way to control initial oscillations is to use chain -thermostats. The keyword tchain determines the number of thermostats -in the particle thermostat. A value of 1 corresponds to the original -Nose-Hoover thermostat. The keyword pchain specifies the number of -thermostats in the chain thermostatting the barostat degrees of -freedom. A value of 0 corresponds to no thermostatting of the -barostat variables. -

    -

    The mtk keyword controls whether or not the correction terms due to -Martyna, Tuckerman, and Klein are included in the equations of motion -(Martyna). Specifying no reproduces the original -Hoover barostat, whose volume probability distribution function -differs from the true NPT and NPH ensembles by a factor of 1/V. Hence -using yes is more correct, but in many cases the difference is -negligible. -

    -

    The keyword tloop can be used to improve the accuracy of integration -scheme at little extra cost. The initial and final updates of the -thermostat variables are broken up into tloop substeps, each of -length dt/tloop. This corresponds to using a first-order -Suzuki-Yoshida scheme (Tuckerman2006). The keyword -ploop does the same thing for the barostat thermostat. -

    -

    The keyword nreset controls how often the reference dimensions used -to define the strain energy are reset. If this keyword is not used, -or is given a value of zero, then the reference dimensions are set to -those of the initial simulation domain and are never changed. If the -simulation domain changes significantly during the simulation, then -the final average pressure tensor will differ significantly from the -specified values of the external stress tensor. A value of nstep -means that every nstep timesteps, the reference dimensions are set -to those of the current simulation domain. -

    -

    The scaleyz, scalexz, and scalexy keywords control whether or -not the corresponding tilt factors are scaled with the associated box -dimensions when barostatting triclinic periodic cells. The default -values yes will turn on scaling, which corresponds to adjusting the -linear dimensions of the cell while preserving its shape. Choosing -no ensures that the tilt factors are not scaled with the box -dimensions. See below for restrictions and default values in different -situations. In older versions of LAMMPS, scaling of tilt factors was -not performed. The old behavior can be recovered by setting all three -scale keywords to no. -

    -

    The flip keyword allows the tilt factors for a triclinic box to -exceed half the distance of the parallel box length, as discussed -below. If the flip value is set to yes, the bound is enforced by -flipping the box when it is exceeded. If the flip value is set to -no, the tilt will continue to change without flipping. Note that if -applied stress induces large deformations (e.g. in a liquid), this -means the box shape can tilt dramatically and LAMMPS will run less -efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. -

    -

    The fixedpoint keyword specifies the fixed point for barostat volume -changes. By default, it is the center of the box. Whatever point is -chosen will not move during the simulation. For example, if the lower -periodic boundaries pass through (0,0,0), and this point is provided -to fixedpoint, then the lower periodic boundaries will remain at -(0,0,0), while the upper periodic boundaries will move twice as -far. In all cases, the particle trajectories are unaffected by the -chosen value, except for a time-dependent constant translation of -positions. -

    -
    - -

    IMPORTANT NOTE: Using a barostat coupled to tilt dimensions xy, -xz, yz can sometimes result in arbitrarily large values of the -tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS -allows the tilt factors to grow a small amount beyond the normal limit -of half the box length (0.6 times the box length), and then performs a -box "flip" to an equivalent periodic cell. See the discussion of the -flip keyword above, to allow this bound to be exceeded, if desired. -

    -

    The flip operation is described in more detail in the doc page for -fix deform. Both the barostat dynamics and the atom -trajectories are unaffected by this operation. However, if a tilt -factor is incremented by a large amount (1.5 times the box length) on -a single timestep, LAMMPS can not accomodate this event and will -terminate the simulation with an error. This error typically indicates -that there is something badly wrong with how the simulation was -constructed, such as specifying values of Pstart that are too far -from the current stress value, or specifying a timestep that is too -large. Triclinic barostatting should be used with care. This also is -true for other barostat styles, although they tend to be more -forgiving of insults. In particular, it is important to recognize that -equilibrium liquids can not support a shear stress and that -equilibrium solids can not support shear stresses that exceed the -yield stress. -

    -

    One exception to this rule is if the 1st dimension in the tilt factor -(x for xy) is non-periodic. In that case, the limits on the tilt -factor are not enforced, since flipping the box in that dimension does -not change the atom positions due to non-periodicity. In this mode, -if you tilt the system to extreme angles, the simulation will simply -become inefficient due to the highly skewed simulation box. -

    -

    IMPORTANT NOTE: Unlike the fix -temp/berendsen command which performs -thermostatting but NO time integration, these fixes perform -thermostatting/barostatting AND time integration. Thus you should not -use any other time integration fix, such as fix nve on -atoms to which this fix is applied. Likewise, fix nvt and fix npt -should not normally be used on atoms that also have their temperature -controlled by another fix - e.g. by fix langevin or fix -temp/rescale commands. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting and barostatting. -

    -
    - -

    These fixes compute a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if one of these two sets of commands had been issued: -

    -
    compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp 
-
    -
    compute fix-ID_temp all temp
-compute fix-ID_press all pressure fix-ID_temp 
-
    -

    See the compute temp and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press". For fix nvt, the group for the new computes -is the same as the fix group. For fix nph and fix npt, the group for -the new computes is "all" since pressure is computed for the entire -system. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -

    Like other fixes that perform thermostatting, fix nvt and fix npt can -be used with compute commands that calculate a -temperature after removing a "bias" from the atom velocities. -E.g. removing the center-of-mass velocity from a group of atoms or -only calculating temperature on the x-component of velocity or only -calculating temperature for atoms in a geometric region. This is not -done by default, but only if the fix_modify command -is used to assign a temperature compute to this fix that includes such -a bias term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    These fixes can be used with either the verlet or respa -integrators. When using one of the barostat fixes -with respa, LAMMPS uses an integrator constructed -according to the following factorization of the Liouville propagator -(for two rRESPA levels): -

    -
    -
    -

    This factorization differs somewhat from that of Tuckerman et al., in that -the barostat is only updated at the outermost rRESPA level, whereas -Tuckerman's factorization requires splitting the pressure into pieces -corresponding to the forces computed at each rRESPA level. In theory, the -latter method will exhibit better numerical stability. In practice, -because Pdamp is normally chosen to be a large multiple of the -outermost rRESPA timestep, the barostat dynamics are not the -limiting factor for numerical stability. Both -factorizations are time-reversible and can be shown to preserve the phase -space measure of the underlying non-Hamiltonian equations of motion. -

    -
    - -

    The fix npt and fix nph commands can be used with rigid bodies or -mixtures of rigid bodies and non-rigid particles (e.g. solvent). But -there are also fix rigid/npt and fix -rigid/nph commands, which are typically a more natural -choice. See the doc page for those commands for more discussion of -the various ways to do this. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    These fixes writes the state of all the thermostat and barostat -variables to binary restart files. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    The fix_modify temp and press options are -supported by these fixes. You can use them to assign a -compute you have defined to this fix which will be used -in its thermostatting or barostatting procedure, as described above. -If you do this, note that the kinetic energy derived from the compute -temperature should be consistent with the virial term computed using -all atoms for the pressure. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. -

    -

    IMPORTANT NOTE: If both the temp and press keywords are used in a -single thermo_modify command (or in two separate commands), then the -order in which the keywords are specified is important. Note that a -pressure compute defines its own temperature -compute as an argument when it is specified. The temp keyword will -override this (for the pressure compute being used by fix npt), but -only if the temp keyword comes after the press keyword. If the -temp keyword comes before the press keyword, then the new pressure -compute specified by the press keyword will be unaffected by the -temp setting. -

    -

    The fix_modify energy option is supported by these -fixes to add the energy change induced by Nose/Hoover thermostatting -and barostatting to the system's potential energy as part of -thermodynamic output. -

    -

    These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various output -commands. The scalar value calculated by -these fixes is "extensive"; the vector values are "intensive". -

    -

    The scalar is the cumulative energy change due to the fix. -

    -

    The vector stores internal Nose/Hoover thermostat and barostat -variables. The number and meaning of the vector values depends on -which fix is used and the settings for keywords tchain and pchain, -which specify the number of Nose/Hoover chains for the thermostat and -barostat. If no thermostatting is done, then tchain is 0. If no -barostatting is done, then pchain is 0. In the following list, -"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in -the barostat. Its value is 0 if no barostat is used, else its value -is 6 if any off-diagonal stress tensor component is barostatted, else -its value is 1 if couple xyz is used or couple xy for a 2d -simulation, otherwise its value is 3. -

    -

    The order of values in the global vector and their meaning is as -follows. The notation means there are tchain values for eta, followed -by tchain for eta_dot, followed by ndof for omega, etc: -

    -
    • eta[tchain] = particle thermostat displacements (unitless) -
    • eta_dot[tchain] = particle thermostat velocities (1/time units) -
    • omega[ndof] = barostat displacements (unitless) -
    • omega_dot[ndof] = barostat velocities (1/time units) -
    • etap[pchain] = barostat thermostat displacements (unitless) -
    • etap_dot[pchain] = barostat thermostat velocities (1/time units) -
    • PE_eta[tchain] = potential energy of each particle thermostat displacement (energy units) -
    • KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units) -
    • PE_omega[ndof] = potential energy of each barostat displacement (energy units) -
    • KE_omega_dot[ndof] = kinetic energy of each barostat velocity (energy units) -
    • PE_etap[pchain] = potential energy of each barostat thermostat displacement (energy units) -
    • KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units) -
    • PE_strain[1] = scalar strain energy (energy units) -
    -

    These fixes can ramp their external temperature and pressure over -multiple runs, using the start and stop keywords of the -run command. See the run command for details of -how to do this. -

    -

    These fixes are not invoked during energy -minimization. -

    -
    - -

    Restrictions: -

    -

    X, y, z cannot be barostatted if the associated dimension is not -periodic. Xy, xz, and yz can only be barostatted if the -simulation domain is triclinic and the 2nd dimension in the keyword -(y dimension in xy) is periodic. Z, xz, and yz, cannot be -barostatted for 2D simulations. The create_box, -read data, and read_restart -commands specify whether the simulation box is orthogonal or -non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz -tilt factors. -

    -

    For the temp keyword, the final Tstop cannot be 0.0 since it would -make the external T = 0.0 at some timestep during the simulation which -is not allowed in the Nose/Hoover formulation. -

    -

    The scaleyz yes and scalexz yes keyword/value pairs can not be used -for 2D simulations. scaleyz yes, scalexz yes, and scalexy yes options -can only be used if the 2nd dimension in the keyword is periodic, -and if the tilt factor is not coupled to the barostat via keywords -tri, yz, xz, and xy. -

    -

    These fixes can be used with dynamic groups as defined by the -group command. Likewise they can be used with groups to -which atoms are added or deleted over time, e.g. a deposition -simulation. However, the conservation properties of the thermostat -and barostat are defined for systems with a static set of atoms. You -may observe odd behavior if the atoms in a group vary dramatically -over time or the atom count becomes very small. -

    -

    Related commands: -

    -

    fix nve, fix_modify, -run_style -

    -

    Default: -

    -

    The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = -ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, -scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and -not coupled to barostat, otherwise no. -

    -
    - - - -

    (Martyna) Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). -

    - - -

    (Parrinello) Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). -

    - - -

    (Tuckerman) Tuckerman, Alejandre, Lopez-Rendon, Jochim, and -Martyna, J Phys A: Math Gen, 39, 5629 (2006). -

    - - -

    (Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). -

    - diff --git a/doc/doc2/fix_nh_eff.html b/doc/doc2/fix_nh_eff.html deleted file mode 100644 index 7d159b4bd6..0000000000 --- a/doc/doc2/fix_nh_eff.html +++ /dev/null @@ -1,158 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nvt/eff command -

    -

    fix npt/eff command -

    -

    fix nph/eff command -

    -

    Syntax: -

    -
    fix ID group-ID style_name keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • style_name = nvt/eff or npt/eff or nph/eff - -
      one or more keyword value pairs may be appended
-keyword = temp or iso or aniso or tri or x or y or z or xy or yz or xz or couple or tchain or pchain or mtk or tloop or ploop or nreset or drag or dilate
-  temp values = Tstart Tstop Tdamp
-    Tstart,Tstop = external temperature at start/end of run
-    Tdamp = temperature damping parameter (time units)
-  iso or aniso or tri values = Pstart Pstop Pdamp
-    Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
-    Pdamp = pressure damping parameter (time units)
-  x or y or z or xy or yz or xz values = Pstart Pstop Pdamp
-    Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
-    Pdamp = stress damping parameter (time units)
-  couple = none or xyz or xy or yz or xz
-  tchain value = length of thermostat chain (1 = single thermostat)
-  pchain values = length of thermostat chain on barostat (0 = no thermostat)
-  mtk value = yes or no = add in MTK adjustment term or not
-  tloop value = number of sub-cycles to perform on thermostat
-  ploop value = number of sub-cycles to perform on barostat thermostat
-  nreset value = reset reference cell every this many timesteps
-  drag value = drag factor added to barostat/thermostat (0.0 = no drag)
-  dilate value = all or partial 
-
      - -
    -

    Examples: -

    -
    fix 1 all nvt/eff temp 300.0 300.0 0.1
-fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
-fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
-fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 
-
    -

    Description: -

    -

    These commands perform time integration on Nose-Hoover style -non-Hamiltonian equations of motion for nuclei and electrons in the -group for the electron force field model. The fixes -are designed to generate positions and velocities sampled from the -canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) -ensembles. This is achieved by adding some dynamic variables which -are coupled to the particle velocities (thermostatting) and simulation -domain dimensions (barostatting). In addition to basic thermostatting -and barostatting, these fixes can also create a chain of thermostats -coupled to the particle thermostat, and another chain of thermostats -coupled to the barostat variables. The barostat can be coupled to the -overall box volume, or to individual dimensions, including the xy, -xz and yz tilt dimensions. The external pressure of the barostat -can be specified as either a scalar pressure (isobaric ensemble) or as -components of a symmetric stress tensor (constant stress ensemble). -When used correctly, the time-averaged temperature and stress tensor -of the particles will match the target values specified by -Tstart/Tstop and Pstart/Pstop. -

    -

    The operation of these fixes is exactly like that described by the -fix nvt, npt, and nph commands, except that the radius -and radial velocity of electrons are also updated. Likewise the -temperature and pressure calculated by the fix, using the computes it -creates (as discussed in the fix nvt, npt, and nph -doc page), are performed with computes that include the eFF contribution -to the temperature or kinetic energy from the electron radial velocity. -

    -

    IMPORTANT NOTE: there are two different pressures that can be reported -for eFF when defining the pair_style (see pair -eff/cut to understand these settings), one -(default) that considers electrons do not contribute radial virial -components (i.e. electrons treated as incompressible 'rigid' spheres) -and one that does. The radial electronic contributions to the virials -are only tallied if the flexible pressure option is set, and this will -affect both global and per-atom quantities. In principle, the true -pressure of a system is somewhere in between the rigid and the -flexible eFF pressures, but, for most cases, the difference between -these two pressures will not be significant over long-term averaged -runs (i.e. even though the energy partitioning changes, the total -energy remains similar). -

    -

    IMPORTANT NOTE: currently, there is no available option for the user -to set or create temperature distributions that include the radial -electronic degrees of freedom with the velocity -command, so the the user must allow for these degrees of freedom to -equilibrate (i.e. equi-partitioning of energy) through time -integration. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    See the doc page for the fix nvt, npt, and nph commands -for details. -

    -

    Restrictions: -

    -

    This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Other restriction discussed on the doc page for the fix nvt, npt, and -nph commands also apply. -

    -

    IMPORTANT NOTE: The temperature for systems (regions or groups) with -only electrons and no nuclei is 0.0 (i.e. not defined) in the current -temperature calculations, a practical example would be a uniform -electron gas or a very hot plasma, where electrons remain delocalized -from the nuclei. This is because, even though electron virials are -included in the temperature calculation, these are averaged over the -nuclear degrees of freedom only. In such cases a corrective term must -be added to the pressure to get the correct kinetic contribution. -

    -

    Related commands: -

    -

    fix nvt, fix nph, fix npt, -fix_modify, run_style -

    -

    Default: -

    -

    The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = -ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none. -

    -
    - - - -

    (Martyna) Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). -

    - - -

    (Parrinello) Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). -

    - - -

    (Tuckerman) Tuckerman, Alejandre, Lopez-Rendon, Jochim, and -Martyna, J Phys A: Math Gen, 39, 5629 (2006). -

    - - -

    (Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). -

    - diff --git a/doc/doc2/fix_nph_asphere.html b/doc/doc2/fix_nph_asphere.html deleted file mode 100644 index a6022e235e..0000000000 --- a/doc/doc2/fix_nph_asphere.html +++ /dev/null @@ -1,159 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nph/asphere command -

    -

    fix nph/asphere/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nph/asphere args keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • nph/asphere = style name of this fix command -
    • additional barostat related keyword/value pairs from the fix nph command can be appended -
    -

    Examples: -

    -
    fix 1 all nph/asphere iso 0.0 0.0 1000.0
-fix 2 all nph/asphere x 5.0 5.0 1000.0
-fix 2 all nph/asphere x 5.0 5.0 1000.0 drag 0.2
-fix 2 water nph/asphere aniso 0.0 0.0 1000.0 dilate partial 
-
    -

    Description: -

    -

    Perform constant NPH integration to update position, velocity, -orientation, and angular velocity each timestep for aspherical or -ellipsoidal particles in the group using a Nose/Hoover pressure -barostat. P is pressure; H is enthalpy. This creates a system -trajectory consistent with the isenthalpic ensemble. -

    -

    This fix differs from the fix nph command, which assumes -point particles and only updates their position and velocity. -

    -

    Additional parameters affecting the barostat are specified by keywords -and values documented with the fix nph command. See, -for example, discussion of the aniso, and dilate keywords. -

    -

    The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPH integration. -

    -

    Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword dilate is specified with a value of partial, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. -

    -
    - -

    This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/asphere" and -"pressure", as if these commands had been issued: -

    -
    compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp 
-
    -

    See the compute temp/asphere and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover barostat to binary -restart files. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    The fix_modify temp and press options are -supported by this fix. You can use them to assign a -compute you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover barostatting to -the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix nph command. -

    -

    This fix can ramp its target pressure over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that atoms store torque and angular momementum and a -quaternion as defined by the atom_style ellipsoid -command. -

    -

    All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. -

    -

    Related commands: -

    -

    fix nph, fix nve_asphere, fix -nvt_asphere, fix -npt_asphere, fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nph_sphere.html b/doc/doc2/fix_nph_sphere.html deleted file mode 100644 index f1b4ef9fcc..0000000000 --- a/doc/doc2/fix_nph_sphere.html +++ /dev/null @@ -1,154 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nph/sphere command -

    -

    fix nph/sphere/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nph/sphere args keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • nph/sphere = style name of this fix command -
    • additional barostat related keyword/value pairs from the fix nph command can be appended -
    -

    Examples: -

    -
    fix 1 all nph/sphere iso 0.0 0.0 1000.0
-fix 2 all nph/sphere x 5.0 5.0 1000.0
-fix 2 all nph/sphere x 5.0 5.0 1000.0 drag 0.2
-fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial 
-
    -

    Description: -

    -

    Perform constant NPH integration to update position, velocity, and -angular velocity each timestep for finite-size spherical particles in -the group using a Nose/Hoover pressure barostat. P is pressure; H is -enthalpy. This creates a system trajectory consistent with the -isenthalpic ensemble. -

    -

    This fix differs from the fix nph command, which assumes -point particles and only updates their position and velocity. -

    -

    Additional parameters affecting the barostat are specified by keywords -and values documented with the fix nph command. See, -for example, discussion of the aniso, and dilate keywords. -

    -

    The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPH integration. -

    -

    Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword dilate is specified with a value of partial, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. -

    -
    - -

    This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/sphere" and -"pressure", as if these commands had been issued: -

    -
    compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp 
-
    -

    See the compute temp/sphere and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover barostat to binary -restart files. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    The fix_modify temp and press options are -supported by this fix. You can use them to assign a -compute you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover barostatting to -the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix nph command. -

    -

    This fix can ramp its target pressure over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the atom_style sphere -command. -

    -

    All particles in the group must be finite-size spheres. They cannot -be point particles. -

    -

    Related commands: -

    -

    fix nph, fix nve_sphere, fix -nvt_sphere, fix npt_sphere, -fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nphug.html b/doc/doc2/fix_nphug.html deleted file mode 100644 index 9fb2140e7f..0000000000 --- a/doc/doc2/fix_nphug.html +++ /dev/null @@ -1,239 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nphug command -

    -

    fix nphug/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nphug keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
      one or more keyword value pairs may be appended
-keyword = temp or iso or aniso or tri or x or y or z or couple or tchain or pchain or mtk or tloop or ploop or nreset or drag or dilate or scaleyz or scalexz or scalexy
-  temp values = Value1 Value2 Tdamp
-    Value1, Value2 = Nose-Hoover target temperatures, ignored by Hugoniostat
-    Tdamp = temperature damping parameter (time units)
-  iso or aniso or tri values = Pstart Pstop Pdamp
-    Pstart,Pstop = scalar external pressures, must be equal (pressure units)
-    Pdamp = pressure damping parameter (time units)
-  x or y or z or xy or yz or xz values = Pstart Pstop Pdamp
-    Pstart,Pstop = external stress tensor components, must be equal (pressure units)
-    Pdamp = stress damping parameter (time units)
-  couple = none or xyz or xy or yz or xz
-  tchain value = length of thermostat chain (1 = single thermostat)
-  pchain values = length of thermostat chain on barostat (0 = no thermostat)
-  mtk value = yes or no = add in MTK adjustment term or not
-  tloop value = number of sub-cycles to perform on thermostat
-  ploop value = number of sub-cycles to perform on barostat thermostat
-  nreset value = reset reference cell every this many timesteps
-  drag value = drag factor added to barostat/thermostat (0.0 = no drag)
-  dilate value = all or partial
-  scaleyz value = yes or no = scale yz with lz
-  scalexz value = yes or no = scale xz with lz
-  scalexy value = yes or no = scale xy with ly 
-
      - -
    -

    Examples: -

    -
    fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
-fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 
-
    -

    Description: -

    -

    This command is a variant of the Nose-Hoover -fix npt fix style. -It performs time integration of the Hugoniostat equations -of motion developed by Ravelo et al. (Ravelo). -These equations compress the system to a state with average -axial stress or pressure equal to the specified target value -and that satisfies the Rankine-Hugoniot (RH) -jump conditions for steady shocks. -

    -

    The compression can be performed -either -hydrostatically (using keyword iso, aniso, or tri) or uniaxially -(using keywords x, y, or z). In the hydrostatic case, -the cell dimensions change dynamically so that the average axial stress -in all three directions converges towards the specified target value. -In the uniaxial case, the chosen cell dimension changes dynamically -so that the average -axial stress in that direction converges towards the target value. The -other two cell dimensions are kept fixed (zero lateral strain). -

    -

    This leads to the following additional restrictions on the keywords: -

    -
    • One and only one of the following keywords should be used: iso, aniso, tri, x, y, z -
    • The specified initial and final target pressures must be the same. -
    • The keywords xy, xz, yz may not be used. -
    • The only admissible value for the couple keyword is xyz, which has the same effect as keyword iso -
    • The temp keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored. -
    -

    Essentially, a Hugoniostat simulation is an NPT simulation in which the -user-specified target temperature is replaced with a time-dependent -target temperature Tt obtained from the following equation: -

    -
    -
    -

    where T and Tt are the instantaneous and target temperatures, -P and P0 are the instantaneous and reference pressures or axial stresses, -depending on whether hydrostatic or uniaxial compression is being -performed, V and V0 are the instantaneous and reference volumes, -E and E0 are the instantaneous and reference internal energy (potential -plus kinetic), Ndof is the number of degrees of freedom used in the -definition of temperature, and kB is the Boltzmann constant. Delta is the -negative deviation of the instantaneous temperature from the target temperature. -When the system reaches a stable equilibrium, the value of Delta should -fluctuate about zero. -

    -

    The values of E0, V0, and P0 are the instantaneous values at the start of -the simulation. These can be overridden using the fix_modify keywords e0, -v0, and p0 described below. -

    -
    - -

    IMPORTANT NOTE: Unlike the fix -temp/berendsen command which performs -thermostatting but NO time integration, this fix performs -thermostatting/barostatting AND time integration. Thus you should not -use any other time integration fix, such as fix nve on -atoms to which this fix is applied. Likewise, this fix should not be -used on atoms that have their temperature controlled by another fix -- e.g. by fix langevin or fix temp/rescale -commands. -

    -
    - -

    This fix computes a temperature and pressure at each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if one of these two sets of commands had been issued: -

    -
    compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp 
-
    -
    compute fix-ID_temp all temp
-compute fix-ID_press all pressure fix-ID_temp 
-
    -

    See the compute temp and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press". The group for -the new computes is "all" since pressure is computed for the entire -system. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the values of E0, V0, and P0, as well as the -state of all the thermostat and barostat -variables to binary restart files. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    The fix_modify e0, v0 and p0 keywords -can be used to define the values of E0, V0, and P0. Note the -the values for e0 and v0 are extensive, and so must correspond -to the total energy and volume of the entire system, not energy and -volume per atom. If any of these quantities are not specified, then the -instantaneous value in the system at the start of the simulation is used. -

    -

    The fix_modify temp and press options are -supported by these fixes. You can use them to assign a -compute you have defined to this fix which will be used -in its thermostatting or barostatting procedure, as described above. -If you do this, note that the kinetic energy derived from the compute -temperature should be consistent with the virial term computed using -all atoms for the pressure. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. -

    -

    The fix_modify energy option is supported by these -fixes to add the energy change induced by Nose/Hoover thermostatting -and barostatting to the system's potential energy as part of -thermodynamic output. Either way, this energy is *not* -included in the definition of internal energy E when calculating the value -of Delta in the above equation. -

    -

    These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various output -commands. The scalar value calculated by -these fixes is "extensive"; the vector values are "intensive". -

    -

    The scalar is the cumulative energy change due to the fix. -

    -

    The vector stores three quantities unique to this fix (Delta, Us, and up), -followed by all the internal Nose/Hoover thermostat and barostat -variables defined for fix_style npt. Delta is the deviation -of the temperature from the target temperature, given by the above equation. -Us and up are the shock and particle velocity corresponding to a steady -shock calculated from the RH conditions. They have units of distance/time. -

    -

    Restrictions: -

    -

    This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    All the usual restrictions for fix_style npt apply, -plus the additional ones mentioned above. -

    -

    Related commands: -

    -

    fix msst, fix npt, fix_modify -

    -

    Default: -

    -

    The keyword defaults are the same as those for fix npt -

    -
    - - - -

    (Ravelo) Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). -

    - diff --git a/doc/doc2/fix_npt_asphere.html b/doc/doc2/fix_npt_asphere.html deleted file mode 100644 index f98e64f146..0000000000 --- a/doc/doc2/fix_npt_asphere.html +++ /dev/null @@ -1,183 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix npt/asphere command -

    -

    fix npt/asphere/omp command -

    -

    Syntax: -

    -
    fix ID group-ID npt/asphere keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • npt/asphere = style name of this fix command -
    • additional thermostat and barostat related keyword/value pairs from the fix npt command can be appended -
    -

    Examples: -

    -
    fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
-fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
-fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
-fix 2 water npt/asphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial 
-
    -

    Description: -

    -

    Perform constant NPT integration to update position, velocity, -orientation, and angular velocity each timestep for aspherical or -ellipsoidal particles in the group using a Nose/Hoover temperature -thermostat and Nose/Hoover pressure barostat. P is pressure; T is -temperature. This creates a system trajectory consistent with the -isothermal-isobaric ensemble. -

    -

    This fix differs from the fix npt command, which -assumes point particles and only updates their position and velocity. -

    -

    The thermostat is applied to both the translational and rotational -degrees of freedom for the aspherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. -

    -

    Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the fix -npt command. See, for example, discussion of the temp, -iso, aniso, and dilate keywords. -

    -

    The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPT integration. -

    -

    Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword dilate is specified with a value of partial, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. -

    -
    - -

    This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/asphere" and -"pressure", as if these commands had been issued: -

    -
    compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp 
-
    -

    See the compute temp/asphere and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover thermostat and barostat -to binary restart files. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    The fix_modify temp and press options are -supported by this fix. You can use them to assign a -compute you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting and -barostatting to the system's potential energy as part of -thermodynamic output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix npt command. -

    -

    This fix can ramp its target temperature and pressure over multiple -runs, using the start and stop keywords of the run -command. See the run command for details of how to do -this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that atoms store torque and angular momementum and a -quaternion as defined by the atom_style ellipsoid -command. -

    -

    All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. -

    -

    Related commands: -

    -

    fix npt, fix nve_asphere, fix -nvt_asphere, fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_npt_sphere.html b/doc/doc2/fix_npt_sphere.html deleted file mode 100644 index ff49496068..0000000000 --- a/doc/doc2/fix_npt_sphere.html +++ /dev/null @@ -1,178 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix npt/sphere command -

    -

    fix npt/sphere/omp command -

    -

    Syntax: -

    -
    fix ID group-ID npt/sphere keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • npt/sphere = style name of this fix command -
    • additional thermostat and barostat related keyword/value pairs from the fix npt command can be appended -
    -

    Examples: -

    -
    fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
-fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
-fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
-fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial 
-
    -

    Description: -

    -

    Perform constant NPT integration to update position, velocity, and -angular velocity each timestep for finite-sizex spherical particles in -the group using a Nose/Hoover temperature thermostat and Nose/Hoover -pressure barostat. P is pressure; T is temperature. This creates a -system trajectory consistent with the isothermal-isobaric ensemble. -

    -

    This fix differs from the fix npt command, which -assumes point particles and only updates their position and velocity. -

    -

    The thermostat is applied to both the translational and rotational -degrees of freedom for the spherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. -

    -

    Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the fix -npt command. See, for example, discussion of the temp, -iso, aniso, and dilate keywords. -

    -

    The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPT integration. -

    -

    Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword dilate is specified with a value of partial, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. -

    -
    - -

    This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/sphere" and -"pressure", as if these commands had been issued: -

    -
    compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp 
-
    -

    See the compute temp/sphere and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover thermostat and barostat -to binary restart files. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    The fix_modify temp and press options are -supported by this fix. You can use them to assign a -compute you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting and -barostatting to the system's potential energy as part of -thermodynamic output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix npt command. -

    -

    This fix can ramp its target temperature and pressure over multiple -runs, using the start and stop keywords of the run -command. See the run command for details of how to do -this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the atom_style sphere -command. -

    -

    All particles in the group must be finite-size spheres. They cannot -be point particles. -

    -

    Related commands: -

    -

    fix npt, fix nve_sphere, fix -nvt_sphere, fix -npt_asphere, fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve.html b/doc/doc2/fix_nve.html deleted file mode 100644 index fbb4520858..0000000000 --- a/doc/doc2/fix_nve.html +++ /dev/null @@ -1,81 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve command -

    -

    fix nve/cuda command -

    -

    fix nve/kk command -

    -

    fix nve/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nve 
-
    -
    • ID, group-ID are documented in fix command -
    • nve = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all nve 
-
    -

    Description: -

    -

    Perform constant NVE integration to update position and velocity for -atoms in the group each timestep. V is volume; E is energy. This -creates a system trajectory consistent with the microcanonical -ensemble. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix nvt, fix npt -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_asphere.html b/doc/doc2/fix_nve_asphere.html deleted file mode 100644 index 8b5ea4a3f5..0000000000 --- a/doc/doc2/fix_nve_asphere.html +++ /dev/null @@ -1,65 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/asphere command -

    -

    Syntax: -

    -
    fix ID group-ID nve/asphere 
-
    -
    • ID, group-ID are documented in fix command -
    • nve/asphere = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all nve/asphere 
-
    -

    Description: -

    -

    Perform constant NVE integration to update position, velocity, -orientation, and angular velocity for aspherical particles in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. -

    -

    This fix differs from the fix nve command, which -assumes point particles and only updates their position and velocity. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that atoms store torque and angular momementum and a -quaternion as defined by the atom_style ellipsoid -command. -

    -

    All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. -

    -

    Related commands: -

    -

    fix nve, fix nve/sphere -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_asphere_noforce.html b/doc/doc2/fix_nve_asphere_noforce.html deleted file mode 100644 index 4dd6f31ad6..0000000000 --- a/doc/doc2/fix_nve_asphere_noforce.html +++ /dev/null @@ -1,70 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/asphere/noforce command -

    -

    Syntax: -

    -
    fix ID group-ID nve/asphere/noforce 
-
    -
    • ID, group-ID are documented in fix command -
    • nve/asphere/noforce = style name of this fix command -
    -

    Examples: -

    -

    fix 1 all nve/asphere/noforce -

    -

    Description: -

    -

    Perform updates of position and orientation, but not velocity or -angular momentum for atoms in the group each timestep. In other -words, the force and torque on the atoms is ignored and their velocity -and angular momentum are not updated. The atom velocities and -angularm momenta are used to update their positions and orientation. -

    -

    This is useful as an implicit time integrator for Fast Lubrication -Dynamics, since the velocity and angular momentum are updated by the -pair_style lubricuteU command. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that atoms store torque and angular momementum and a -quaternion as defined by the atom_style ellipsoid -command. -

    -

    All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. -

    -

    Related commands: -

    -

    fix nve/noforce, fix -nve/asphere -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_body.html b/doc/doc2/fix_nve_body.html deleted file mode 100644 index fc7fe3dd6a..0000000000 --- a/doc/doc2/fix_nve_body.html +++ /dev/null @@ -1,67 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/body command -

    -

    Syntax: -

    -
    fix ID group-ID nve/body 
-
    -
    • ID, group-ID are documented in fix command -
    • nve/body = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all nve/body 
-
    -

    Description: -

    -

    Perform constant NVE integration to update position, velocity, -orientation, and angular velocity for body particles in the group each -timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See Section_howto -14 of the manual and the body -doc page for more details on using body particles. -

    -

    This fix differs from the fix nve command, which -assumes point particles and only updates their position and velocity. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that atoms store torque and angular momementum and a -quaternion as defined by the atom_style body -command. -

    -

    All particles in the group must be body particles. They cannot be -point particles. -

    -

    Related commands: -

    -

    fix nve, fix nve/sphere, fix -nve/asphere -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_eff.html b/doc/doc2/fix_nve_eff.html deleted file mode 100644 index 80b1509242..0000000000 --- a/doc/doc2/fix_nve_eff.html +++ /dev/null @@ -1,59 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/eff command -

    -

    Syntax: -

    -
    fix ID group-ID nve/eff 
-
    -
    • ID, group-ID are documented in fix command -
    • nve/eff = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all nve/eff 
-
    -

    Description: -

    -

    Perform constant NVE integration to update position and velocity for -nuclei and electrons in the group for the electron force -field model. V is volume; E is energy. This creates a -system trajectory consistent with the microcanonical ensemble. -

    -

    The operation of this fix is exactly like that described by the fix -nve command, except that the radius and radial velocity -of electrons are also updated. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix nve, fix nvt/eff, fix -npt/eff -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_limit.html b/doc/doc2/fix_nve_limit.html deleted file mode 100644 index 13b40bb9e6..0000000000 --- a/doc/doc2/fix_nve_limit.html +++ /dev/null @@ -1,91 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/limit command -

    -

    Syntax: -

    -
    fix ID group-ID nve/limit xmax 
-
    -
    • ID, group-ID are documented in fix command -
    • nve = style name of this fix command -
    • xmax = maximum distance an atom can move in one timestep (distance units) -
    -

    Examples: -

    -
    fix 1 all nve/limit 0.1 
-
    -

    Description: -

    -

    Perform constant NVE updates of position and velocity for atoms in the -group each timestep. A limit is imposed on the maximum distance an -atom can move in one timestep. This is useful when starting a -simulation with a configuration containing highly overlapped atoms. -Normally this would generate huge forces which would blow atoms out of -the simulation box, causing LAMMPS to stop with an error. -

    -

    Using this fix can overcome that problem. Forces on atoms must still -be computable (which typically means 2 atoms must have a separation -distance > 0.0). But large velocities generated by large forces are -reset to a value that corresponds to a displacement of length xmax -in a single timestep. Xmax is specified in distance units; see the -units command for details. The value of xmax should be -consistent with the neighbor skin distance and the frequency of -neighbor list re-building, so that pairwise interactions are not -missed on successive timesteps as atoms move. See the -neighbor and neigh_modify commands -for details. -

    -

    Note that if a velocity reset occurs the integrator will not conserve -energy. On steps where no velocity resets occur, this integrator is -exactly like the fix nve command. Since forces are -unaltered, pressures computed by thermodynamic output will still be -very large for overlapped configurations. -

    -

    IMPORTANT NOTE: You should not use fix shake in -conjunction with this fix. That is because fix shake applies -contraint forces based on the predicted postitions of atoms after the -next timestep. It has no way of knowing the timestep may change due -to this fix, which will cause the constraint forces to be invalid. A -better strategy is to turn off fix shake when performing initial -dynamics that need this fix, then turn fix shake on when doing normal -dynamics with a fixed-size timestep. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -count of how many updates of atom's velocity/position were limited by -the maximum distance criterion. This should be roughly the number of -atoms so affected, except that updates occur at both the beginning and -end of a timestep in a velocity Verlet timestepping algorithm. This -is a cumulative quantity for the current run, but is re-initialized to -zero each time a run is performed. The scalar value calculated by -this fix is "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix nve, fix nve/noforce, -pair_style soft -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_line.html b/doc/doc2/fix_nve_line.html deleted file mode 100644 index 9b18cfeaa3..0000000000 --- a/doc/doc2/fix_nve_line.html +++ /dev/null @@ -1,62 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/line command -

    -

    Syntax: -

    -
    fix ID group-ID nve/line 
-
    -
    • ID, group-ID are documented in fix command -
    • nve/line = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all nve/line 
-
    -

    Description: -

    -

    Perform constant NVE integration to update position, velocity, -orientation, and angular velocity for line segment particles in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See -Section_howto 14 of the manual for an overview of -using line segment particles. -

    -

    This fix differs from the fix nve command, which -assumes point particles and only updates their position and velocity. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that particles be line segments as defined by the -atom_style line command. -

    -

    Related commands: -

    -

    fix nve, fix nve/asphere -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_noforce.html b/doc/doc2/fix_nve_noforce.html deleted file mode 100644 index 8150e5668a..0000000000 --- a/doc/doc2/fix_nve_noforce.html +++ /dev/null @@ -1,59 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/noforce command -

    -

    Syntax: -

    -
    fix ID group-ID nve 
-
    -
    • ID, group-ID are documented in fix command -
    • nve/noforce = style name of this fix command -
    -

    Examples: -

    -
    fix 3 wall nve/noforce 
-
    -

    Description: -

    -

    Perform updates of position, but not velocity for atoms in the group -each timestep. In other words, the force on the atoms is ignored and -their velocity is not updated. The atom velocities are used to update -their positions. -

    -

    This can be useful for wall atoms, when you set their velocities, and -want the wall to move (or stay stationary) in a prescribed fashion. -

    -

    This can also be accomplished via the fix setforce -command, but with fix nve/noforce, the forces on the wall atoms are -unchanged, and can thus be printed by the dump command or -queried with an equal-style variable that uses the -fcm() group function to compute the total force on the group of atoms. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix nve -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_sphere.html b/doc/doc2/fix_nve_sphere.html deleted file mode 100644 index 4ac5df95aa..0000000000 --- a/doc/doc2/fix_nve_sphere.html +++ /dev/null @@ -1,106 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/sphere command -

    -

    fix nve/sphere/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nve/sphere 
-
    -
    • ID, group-ID are documented in fix command - -
    • nve/sphere = style name of this fix command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = update - -
        update value = dipole
-    dipole = update orientation of dipole moment during integration 
-
      - -
    -

    Examples: -

    -
    fix 1 all nve/sphere
-fix 1 all nve/sphere update dipole 
-
    -

    Description: -

    -

    Perform constant NVE integration to update position, velocity, and -angular velocity for finite-size spherical particles in the group each -timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. -

    -

    This fix differs from the fix nve command, which -assumes point particles and only updates their position and velocity. -

    -

    If the update keyword is used with the dipole value, then the -orientation of the dipole moment of each particle is also updated -during the time integration. This option should be used for models -where a dipole moment is assigned to particles via use of the -atom_style dipole command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the atom_style sphere -command. If the dipole keyword is used, then they must also store a -dipole moment as defined by the atom_style dipole -command. -

    -

    All particles in the group must be finite-size spheres. They cannot -be point particles. -

    -

    Related commands: -

    -

    fix nve, fix nve/asphere -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nve_tri.html b/doc/doc2/fix_nve_tri.html deleted file mode 100644 index de9d25b43f..0000000000 --- a/doc/doc2/fix_nve_tri.html +++ /dev/null @@ -1,62 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nve/tri command -

    -

    Syntax: -

    -
    fix ID group-ID nve/tri 
-
    -
    • ID, group-ID are documented in fix command -
    • nve/tri = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all nve/tri 
-
    -

    Description: -

    -

    Perform constant NVE integration to update position, velocity, -orientation, and angular momentum for triangular particles in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See -Section_howto 14 of the manual for an overview of -using triangular particles. -

    -

    This fix differs from the fix nve command, which -assumes point particles and only updates their position and velocity. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that particles be triangles as defined by the -atom_style tri command. -

    -

    Related commands: -

    -

    fix nve, fix nve/asphere -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nvt_asphere.html b/doc/doc2/fix_nvt_asphere.html deleted file mode 100644 index 6320f401b0..0000000000 --- a/doc/doc2/fix_nvt_asphere.html +++ /dev/null @@ -1,159 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nvt/asphere command -

    -

    fix nvt/asphere/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nvt/asphere keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • nvt/asphere = style name of this fix command -
    • additional thermostat related keyword/value pairs from the fix nvt command can be appended -
    -

    Examples: -

    -
    fix 1 all nvt/asphere temp 300.0 300.0 100.0
-fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2 
-
    -

    Description: -

    -

    Perform constant NVT integration to update position, velocity, -orientation, and angular velocity each timestep for aspherical or -ellipsoidal particles in the group using a Nose/Hoover temperature -thermostat. V is volume; T is temperature. This creates a system -trajectory consistent with the canonical ensemble. -

    -

    This fix differs from the fix nvt command, which -assumes point particles and only updates their position and velocity. -

    -

    The thermostat is applied to both the translational and rotational -degrees of freedom for the aspherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. -

    -

    Additional parameters affecting the thermostat are specified by -keywords and values documented with the fix nvt -command. See, for example, discussion of the temp and drag -keywords. -

    -

    This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/asphere", as if this command -had been issued: -

    -
    compute fix-ID_temp group-ID temp/asphere 
-
    -

    See the compute temp/asphere command for -details. Note that the ID of the new compute is the fix-ID + -underscore + "temp", and the group for the new compute is the same as -the fix group. -

    -

    Note that this is NOT the compute used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -compute_modify command or print this temperature -during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp will have no -effect on this fix. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover thermostat to binary -restart files. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a compute you have -defined to this fix which will be used in its thermostatting -procedure. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix nvt command. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires that atoms store torque and angular momementum and a -quaternion as defined by the atom_style ellipsoid -command. -

    -

    All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. -

    -

    Related commands: -

    -

    fix nvt, fix nve_asphere, fix -npt_asphere, fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_nvt_sllod.html b/doc/doc2/fix_nvt_sllod.html deleted file mode 100644 index b4bca0eaf4..0000000000 --- a/doc/doc2/fix_nvt_sllod.html +++ /dev/null @@ -1,187 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nvt/sllod command -

    -

    fix nvt/sllod/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nvt/sllod keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • nvt/sllod = style name of this fix command -
    • additional thermostat related keyword/value pairs from the fix nvt command can be appended -
    -

    Examples: -

    -
    fix 1 all nvt/sllod temp 300.0 300.0 100.0
-fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2 
-
    -

    Description: -

    -

    Perform constant NVT integration to update positions and velocities -each timestep for atoms in the group using a Nose/Hoover temperature -thermostat. V is volume; T is temperature. This creates a system -trajectory consistent with the canonical ensemble. -

    -

    This thermostat is used for a simulation box that is changing size -and/or shape, for example in a non-equilibrium MD (NEMD) simulation. -The size/shape change is induced by use of the fix -deform command, so each point in the simulation box -can be thought of as having a "streaming" velocity. This -position-dependent streaming velocity is subtracted from each atom's -actual velocity to yield a thermal velocity which is used for -temperature computation and thermostatting. For example, if the box -is being sheared in x, relative to y, then points at the bottom of the -box (low y) have a small x velocity, while points at the top of the -box (hi y) have a large x velocity. These velocities do not -contribute to the thermal "temperature" of the atom. -

    -

    IMPORTANT NOTE: Fix deform has an option for -remapping either atom coordinates or velocities to the changing -simulation box. To use fix nvt/sllod, fix deform should NOT remap -atom positions, because fix nvt/sllod adjusts the atom positions and -velocities to create a velocity profile that matches the changing box -size/shape. Fix deform SHOULD remap atom velocities when atoms cross -periodic boundaries since that is consistent with maintaining the -velocity profile created by fix nvt/sllod. LAMMPS will give an -error if this setting is not consistent. -

    -

    The SLLOD equations of motion, originally proposed by Hoover and Ladd -(see (Evans and Morriss)), were proven to be equivalent to -Newton's equations of motion for shear flow by (Evans and -Morriss). They were later shown to generate the desired -velocity gradient and the correct production of work by stresses for -all forms of homogeneous flow by (Daivis and Todd). As -implemented in LAMMPS, they are coupled to a Nose/Hoover chain -thermostat in a velocity Verlet formulation, closely following the -implementation used for the fix nvt command. -

    -

    Additional parameters affecting the thermostat are specified by -keywords and values documented with the fix nvt -command. See, for example, discussion of the temp and drag -keywords. -

    -

    This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/deform", as if this command had -been issued: -

    -
    compute fix-ID_temp group-ID temp/deform 
-
    -

    See the compute temp/deform command for -details. Note that the ID of the new compute is the fix-ID + -underscore + "temp", and the group for the new compute is the same as -the fix group. -

    -

    Note that this is NOT the compute used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -compute_modify command or print this temperature -during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp will have no -effect on this fix. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover thermostat to binary -restart files. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a compute you have -defined to this fix which will be used in its thermostatting -procedure. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix nvt command. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix works best without Nose-Hoover chain thermostats, i.e. using -tchain = 1. Setting tchain to larger values can result in poor -equilibration. -

    -

    Related commands: -

    -

    fix nve, fix nvt, fix -temp/rescale, fix langevin, -fix_modify, compute -temp/deform -

    -

    Default: -

    -

    Same as fix nvt, except tchain = 1. -

    -
    - - - -

    (Evans and Morriss) Evans and Morriss, Phys Rev A, 30, 1528 (1984). -

    - - -

    (Daivis and Todd) Daivis and Todd, J Chem Phys, 124, 194103 (2006). -

    - diff --git a/doc/doc2/fix_nvt_sllod_eff.html b/doc/doc2/fix_nvt_sllod_eff.html deleted file mode 100644 index 072b124356..0000000000 --- a/doc/doc2/fix_nvt_sllod_eff.html +++ /dev/null @@ -1,100 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nvt/sllod/eff command -

    -

    Syntax: -

    -
    fix ID group-ID nvt/sllod/eff keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • nvt/sllod/eff = style name of this fix command -
    • additional thermostat related keyword/value pairs from the fix nvt/eff command can be appended -
    -

    Examples: -

    -
    fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
-fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2 
-
    -

    Description: -

    -

    Perform constant NVT integration to update positions and velocities -each timestep for nuclei and electrons in the group for the electron -force field model, using a Nose/Hoover temperature -thermostat. V is volume; T is temperature. This creates a system -trajectory consistent with the canonical ensemble. -

    -

    The operation of this fix is exactly like that described by the fix -nvt/sllod command, except that the radius and -radial velocity of electrons are also updated and thermostatted. -Likewise the temperature calculated by the fix, using the compute it -creates (as discussed in the fix nvt, npt, and nph doc -page), is performed with a compute -temp/deform/eff commmand that includes -the eFF contribution to the temperature from the electron radial -velocity. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover thermostat to binary -restart files. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a compute you have -defined to this fix which will be used in its thermostatting -procedure. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix nvt/eff command. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix works best without Nose-Hoover chain thermostats, i.e. using -tchain = 1. Setting tchain to larger values can result in poor -equilibration. -

    -

    Related commands: -

    -

    fix nve/eff, fix nvt/eff, fix -langevin/eff, fix -nvt/sllod, fix_modify, compute -temp/deform/eff -

    -

    Default: -

    -

    Same as fix nvt/eff, except tchain = 1. -

    -
    - - - -

    (Tuckerman) Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, -106, 5615 (1997). -

    - diff --git a/doc/doc2/fix_nvt_sphere.html b/doc/doc2/fix_nvt_sphere.html deleted file mode 100644 index 574a1a04c4..0000000000 --- a/doc/doc2/fix_nvt_sphere.html +++ /dev/null @@ -1,155 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix nvt/sphere command -

    -

    fix nvt/sphere/omp command -

    -

    Syntax: -

    -
    fix ID group-ID nvt/sphere keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • nvt/sphere = style name of this fix command -
    • additional thermostat related keyword/value pairs from the fix nvt command can be appended -
    -

    Examples: -

    -
    fix 1 all nvt/sphere temp 300.0 300.0 100.0
-fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 
-
    -

    Description: -

    -

    Perform constant NVT integration to update position, velocity, and -angular velocity each timestep for finite-size spherical particles in -the group using a Nose/Hoover temperature thermostat. V is volume; T -is temperature. This creates a system trajectory consistent with the -canonical ensemble. -

    -

    This fix differs from the fix nvt command, which -assumes point particles and only updates their position and velocity. -

    -

    The thermostat is applied to both the translational and rotational -degrees of freedom for the spherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. -

    -

    Additional parameters affecting the thermostat are specified by -keywords and values documented with the fix nvt -command. See, for example, discussion of the temp and drag -keywords. -

    -

    This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/sphere", as if this command -had been issued: -

    -
    compute fix-ID_temp group-ID temp/sphere 
-
    -

    See the compute temp/sphere command for -details. Note that the ID of the new compute is the fix-ID + -underscore + "temp", and the group for the new compute is the same as -the fix group. -

    -

    Note that this is NOT the compute used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -compute_modify command or print this temperature -during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp will have no -effect on this fix. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the state of the Nose/Hoover thermostat to binary -restart files. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a compute you have -defined to this fix which will be used in its thermostatting -procedure. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes the same global scalar and global vector of -quantities as does the fix nvt command. -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the atom_style sphere -command. -

    -

    All particles in the group must be finite-size spheres. They cannot -be point particles. -

    -

    Related commands: -

    -

    fix nvt, fix nve_sphere, fix -nvt_asphere, fix -npt_sphere, fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_oneway.html b/doc/doc2/fix_oneway.html deleted file mode 100644 index 9b48b802b0..0000000000 --- a/doc/doc2/fix_oneway.html +++ /dev/null @@ -1,69 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix oneway command -

    -

    Syntax: -

    -
    fix ID group-ID oneway N region-ID direction 
-
    -
    • ID, group-ID are documented in fix command - -
    • oneway = style name of this fix command - -
    • N = apply this fix every this many timesteps - -
    • region-ID = ID of region where fix is active - -
    • direction = x or -x or y or -y or z or -z = coordinate and direction of the oneway constraint - - -
    -

    Examples: -

    -
    fix ions oneway 10 semi -x
-fix all oneway 1 left -z
-fix all oneway 1 right z 
-
    -

    Description: -

    -

    Enforce that particles in the group and in a given region can only -move in one direction. This is done by reversing a particle's -velocity component, if it has the wrong sign in the specified -dimension. The effect is that the particle moves in one direction -only. -

    -

    This can be used, for example, as a simple model of a semi-permeable -membrane, or as an implementation of Maxwell's demon. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix wall/reflect command -

    -

    Default: none -

    -
    - - diff --git a/doc/doc2/fix_orient_fcc.html b/doc/doc2/fix_orient_fcc.html deleted file mode 100644 index f9d97dad88..0000000000 --- a/doc/doc2/fix_orient_fcc.html +++ /dev/null @@ -1,188 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix orient/fcc command -

    -
    fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1 
-
    -
    • ID, group-ID are documented in fix command -
    • nstats = print stats every this many steps, 0 = never -
    • dir = 0/1 for which crystal is used as reference -
    • alat = fcc cubic lattice constant (distance units) -
    • dE = energy added to each atom (energy units) -
    • cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi -
    • file0,file1 = files that specify orientation of each grain -
    -

    Examples: -

    -
    fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec 
-
    -

    Description: -

    -

    The fix applies an orientation-dependent force to atoms near a planar -grain boundary which can be used to induce grain boundary migration -(in the direction perpendicular to the grain boundary plane). The -motivation and explanation of this force and its application are -described in (Janssens). The force is only applied to -atoms in the fix group. -

    -

    The basic idea is that atoms in one grain (on one side of the -boundary) have a potential energy dE added to them. Atoms in the -other grain have 0.0 potential energy added. Atoms near the boundary -(whose neighbor environment is intermediate between the two grain -orientations) have an energy between 0.0 and dE added. This creates -an effective driving force to reduce the potential energy of atoms -near the boundary by pushing them towards one of the grain -orientations. For dir = 1 and dE > 0, the boundary will thus move so -that the grain described by file0 grows and the grain described by -file1 shrinks. Thus this fix is designed for simulations of two-grain -systems, either with one grain boundary and free surfaces parallel to -the boundary, or a system with periodic boundary conditions and two -equal and opposite grain boundaries. In either case, the entire -system can displace during the simulation, and such motion should be -accounted for in measuring the grain boundary velocity. -

    -

    The potential energy added to atom I is given by these formulas -

    -
    -
    -

    which are fully explained in (Janssens). The order -parameter Xi for atom I in equation (1) is a sum over the 12 nearest -neighbors of atom I. Rj is the vector from atom I to its neighbor J, -and RIj is a vector in the reference (perfect) crystal. That is, if -dir = 0/1, then RIj is a vector to an atom coord from file 0/1. -Equation (2) gives the expected value of the order parameter XiIJ in -the other grain. Hi and lo cutoffs are defined in equations (3) and -(4), using the input parameters cutlo and cuthi as thresholds to -avoid adding grain boundary energy when the deviation in the order -parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a -perfect crystal). The added potential energy Ui for atom I is given -in equation (6) where it is interpolated between 0 and dE using the -two threshold Xi values and the Wi value of equation (5). -

    -

    The derivative of this energy expression gives the force on each atom -which thus depends on the orientation of its neighbors relative to the -2 grain orientations. Only atoms near the grain boundary feel a net -force which tends to drive them to one of the two grain orientations. -

    -

    In equation (1), the reference vector used for each neighbor is the -reference vector closest to the actual neighbor position. This means -it is possible two different neighbors will use the same reference -vector. In such cases, the atom in question is far from a perfect -orientation and will likely receive the full dE addition, so the -effect of duplicate reference vector usage is small. -

    -

    The dir parameter determines which grain wants to grow at the -expense of the other. A value of 0 means the first grain will shrink; -a value of 1 means it will grow. This assumes that dE is positive. -The reverse will be true if dE is negative. -

    -

    The alat parameter is the cubic lattice constant for the fcc -material and is only used to compute a cutoff distance of 1.57 * alat -/ sqrt(2) for finding the 12 nearest neighbors of each atom (which -should be valid for an fcc crystal). A longer/shorter cutoff can be -imposed by adjusting alat. If a particular atom has less than 12 -neighbors within the cutoff, the order parameter of equation (1) is -effectively multiplied by 12 divided by the actual number of neighbors -within the cutoff. -

    -

    The dE parameter is the maximum amount of additional energy added to -each atom in the grain which wants to shrink. -

    -

    The cutlo and cuthi parameters are used to reduce the force added -to bulk atoms in each grain far away from the boundary. An atom in -the bulk surrounded by neighbors at the ideal grain orientation would -compute an order parameter of 0 or 1 and have no force added. -However, thermal vibrations in the solid will cause the order -parameters to be greater than 0 or less than 1. The cutoff parameters -mask this effect, allowing forces to only be added to atoms with -order-parameters between the cutoff values. -

    -

    File0 and file1 are filenames for the two grains which each -contain 6 vectors (6 lines with 3 values per line) which specify the -grain orientations. Each vector is a displacement from a central atom -(0,0,0) to a nearest neighbor atom in an fcc lattice at the proper -orientation. The vector lengths should all be identical since an fcc -lattice has a coordination number of 12. Only 6 are listed due to -symmetry, so the list must include one from each pair of -equal-and-opposite neighbors. A pair of orientation files for a -Sigma=5 tilt boundary are show below. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the potential energy of atom interactions with the grain -boundary driving force to the system's potential energy as part of -thermodynamic output. -

    -

    This fix calculates a global scalar which can be accessed by various -output commands. The scalar is the -potential energy change due to this fix. The scalar value calculated -by this fix is "extensive". -

    -

    This fix also calculates a per-atom array which can be accessed by -various output commands. The array -stores the order parameter Xi and normalized order parameter (0 to 1) -for each atom. The per-atom values can be accessed on any timestep. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix should only be used with fcc lattices. -

    -

    Related commands: -

    -

    fix_modify -

    -

    Default: none -

    -
    - - - -

    (Janssens) Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature -Materials, 5, 124-127 (2006). -

    -
    - -

    For illustration purposes, here are example files that specify a -Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706 -Angs. -

    -

    file0: -

    -
         0.798410432046075    1.785300000000000    1.596820864092150
-    -0.798410432046075    1.785300000000000   -1.596820864092150
-     2.395231296138225    0.000000000000000    0.798410432046075
-     0.798410432046075    0.000000000000000   -2.395231296138225
-     1.596820864092150    1.785300000000000   -0.798410432046075
-     1.596820864092150   -1.785300000000000   -0.798410432046075 
-
    -

    file1: -

    -
        -0.798410432046075    1.785300000000000    1.596820864092150
-     0.798410432046075    1.785300000000000   -1.596820864092150
-     0.798410432046075    0.000000000000000    2.395231296138225
-     2.395231296138225    0.000000000000000   -0.798410432046075
-     1.596820864092150    1.785300000000000    0.798410432046075
-     1.596820864092150   -1.785300000000000    0.798410432046075 
-
    - diff --git a/doc/doc2/fix_phonon.html b/doc/doc2/fix_phonon.html deleted file mode 100644 index 3193e18d96..0000000000 --- a/doc/doc2/fix_phonon.html +++ /dev/null @@ -1,221 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix phonon command -

    -

    Syntax: -

    -
    fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • phonon = style name of this fix command - -
    • N = measure the Green's function every this many timesteps - -
    • Noutput = output the dynamical matrix every this many measurements - -
    • Nwait = wait this many timesteps before measuring - -
    • map_file = file or GAMMA - -
        file is the file that contains the mapping info between atom ID and the lattice indices. 
-
      -
        GAMMA flags to treate the whole simulation box as a unit cell, so that the mapping
-  info can be generated internally. In this case, dynamical matrix at only the gamma-point
-  will/can be evaluated. 
-
      -
    • prefix = prefix for output files - -
    • one or none keyword/value pairs may be appended - -
    • keyword = sysdim or nasr - -
        sysdim value = d
-    d = dimension of the system, usually the same as the MD model dimension
-  nasr value = n
-    n = number of iterations to enforce the acoustic sum rule 
-
      - -
    -

    Examples: -

    -
    fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1
-fix 1 all phonon 20 5000 200000 map.in EAM3D
-fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 
-
    -

    Description: -

    -

    Calculate the dynamical matrix from molecular dynamics simulations -based on fluctuation-dissipation theory for a group of atoms. -

    -

    Consider a crystal with N unit cells in three dimensions labelled l -= (l1,l2,l3) where li -are integers. Each unit cell is defined by three linearly independent -vectors a1, a2, a3 forming a -parallelipiped, containing K basis atoms labelled k. -

    -

    Based on fluctuation-dissipation theory, the force constant -coefficients of the system in reciprocal space are given by -(Campañá , Kong) -

    Φkα,k'β(q) = -kBT -G-1kα,k'β(q),
    -

    -

    where G is the Green's functions coefficients given by -

    -
    Gkα,k'β(q) = -<ukα(q)•uk'β*(q)>,
    - -

    where <...> denotes the ensemble average, and -

    ukα(q) = ∑l -ulkα exp(iqrl)
    -

    -

    is the α component of the atomic displacement for the kth atom -in the unit cell in reciprocal space at q. In practice, the Green's -functions coefficients can also be measured according to the following -formula, -

    -
    Gkα,k'β(q) = -<Rkα(q)•R*k'β(q)> -- <R>kα(q)•<R>*k'β(q), -
    - -

    where R is the instantaneous positions of atoms, and <R> is the -averaged atomic positions. It gives essentially the same results as -the displacement method and is easier to implement in an MD code. -

    -

    Once the force constant matrix is known, the dynamical matrix D can -then be obtained by -

    -
    Dkα, k'β(q) = (mkmk')-1/2 Φkα,k'β(q)
    - -

    whose eigenvalues are exactly the phonon frequencies at q. -

    -

    This fix uses positions of atoms in the specified group and calculates -two-point correlations. To achieve this. the positions of the atoms -are examined every Nevery steps and are Fourier-transformed into -reciprocal space, where the averaging process and correlation -computation is then done. After every Noutput measurements, the -matrix G(q) is calculated and inverted to obtain the elastic -stiffness coefficients. The dynamical matrices are then constructed -and written to prefix.bin.timestep files in binary format and to the -file prefix.log for each wavevector q. -

    -

    A detailed description of this method can be found in -(Kong2011). -

    -

    The sysdim keyword is optional. If specified with a value smaller -than the dimensionality of the LAMMPS simulation, its value is used -for the dynamical matrix calculation. For example, using LAMMPS ot -model a 2D or 3D system, the phonon dispersion of a 1D atomic chain -can be computed using sysdim = 1. -

    -

    The nasr keyword is optional. An iterative procedure is employed to -enforce the acoustic sum rule on Φ at Γ, and the number -provided by keyword nasr gives the total number of iterations. For a -system whose unit cell has only one atom, nasr = 1 is sufficient; -for other systems, nasr = 10 is typically sufficient. -

    -

    The map_file contains the mapping information between the lattice -indices and the atom IDs, which tells the code which atom sits at -which lattice point; the lattice indices start from 0. An auxiliary -code, latgen, can be employed to -generate the compatible map file for various crystals. -

    -

    In case one simulates an aperiodic system, where the whole simulation box -is treated as a unit cell, one can set map_file as GAMMA, so that the mapping -info will be generated internally and a file is not needed. In this case, the -dynamical matrix at only the gamma-point will/can be evaluated. Please keep in -mind that fix-phonon is designed for cyrstals, it will be inefficient and -even degrade the performance of lammps in case the unit cell is too large. -

    -

    The calculated dynamical matrix elements are written out in -energy/distance^2/mass units. The coordinates for q -points in the log file is in the units of the basis vectors of the -corresponding reciprocal lattice. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to change the temperature compute from thermo_temp -to the one that reflects the true temperature of atoms in the group. -

    -

    No global scalar or vector or per-atom quantities are stored by this -fix for access by various output commands. -

    -

    Instead, this fix outputs its initialization information (including -mapping information) and the calculated dynamical matrices to the file -prefix.log, with the specified prefix. The dynamical matrices are -also written to files prefix.bin.timestep in binary format. These -can be read by the post-processing tool in tools/phonon to compute the -phonon density of states and/or phonon dispersion curves. -

    -

    No parameter of this fix can be used with the start/stop keywords -of the run command. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix assumes a crystalline system with periodical lattice. The -temperature of the system should not exceed the melting temperature to -keep the system in its solid state. -

    -

    This fix is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix requires LAMMPS be built with an FFT library. See the -Making LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute msd -

    -

    Default: -

    -

    The option defaults are sysdim = the same dimemsion as specified by -the dimension command, and nasr = 20. -

    -
    - - - -

    (Campañá) C. Campañá and -M. H. Müser, Practical Green's function approach to the -simulation of elastic semi-infinite solids, Phys. Rev. B [74], -075420 (2006) -

    - - -

    (Kong) L.T. Kong, G. Bartels, C. Campañá, -C. Denniston, and Martin H. Müser, Implementation of Green's -function molecular dynamics: An extension to LAMMPS, Computer -Physics Communications [180](6):1004-1010 -(2009). -

    -

    L.T. Kong, C. Denniston, and Martin H. Müser, -An improved version of the Green's function molecular dynamics -method, Computer Physics Communications [182](2):540-541 -(2011). -

    - - -

    (Kong2011) L.T. Kong, Phonon dispersion measured directly from -molecular dynamics simulations, Computer Physics Communications -[182](10):2201-2207, -(2011). -

    - diff --git a/doc/doc2/fix_pimd.html b/doc/doc2/fix_pimd.html deleted file mode 100644 index 44da3e9b4d..0000000000 --- a/doc/doc2/fix_pimd.html +++ /dev/null @@ -1,195 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix pimd command -

    -

    Syntax: -

    -
    fix ID group-ID pimd keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • pimd = style name of this fix command - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = method or fmass or sp or temp or nhc - -
        method value = pimd or nmpimd or cmd
-  fmass value = scaling factor on mass
-  sp value = scaling factor on Planck constant
-  temp value = temperature (temperarate units)
-  nhc value = Nc = number of chains in Nose-Hoover thermostat 
-
      - -
    -

    Examples: -

    -
    fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4 
-
    -

    Description: -

    -

    This command performs quantum molecular dynamics simulations based on -the Feynman path integral to include effects of tunneling and -zero-point motion. In this formalism, the isomorphism of a quantum -partition function for the original system to a classical partition -function for a ring-polymer system is exploited, to efficiently sample -configurations from the canonical ensemble (Feynman). -The classical partition function and its components are given -by the following equations: -

    -
    -
    -

    The interested user is referred to any of the numerous references on -this methodology, but briefly, each quantum particle in a path -integral simulation is represented by a ring-polymer of P quasi-beads, -labeled from 1 to P. During the simulation, each quasi-bead interacts -with beads on the other ring-polymers with the same imaginary time -index (the second term in the effective potential above). The -quasi-beads also interact with the two neighboring quasi-beads through -the spring potential in imaginary-time space (first term in effective -potential). To sample the canonical ensemble, a Nose-Hoover massive -chain thermostat is applied (Tuckerman). With the -massive chain algorithm, a chain of NH thermostats is coupled to each -degree of freedom for each quasi-bead. The keyword temp sets the -target temperature for the system and the keyword nhc sets the -number Nc of thermostats in each chain. For example, for a -simulation of N particles with P beads in each ring-polymer, the total -number of NH thermostats would be 3 x N x P x Nc. -

    -

    IMPORTANT NOTE: This fix implements a complete velocity-verlet -integrator combined with NH massive chain thermostat, so no -other time integration fix should be used. -

    -

    The method keyword determines what style of PIMD is performed. A -value of pimd is standard PIMD. A value of nmpimd is for -normal-mode PIMD. A value of cmd is for centroid molecular dynamics -(CMD). The difference between the styles is as follows. -

    -

    In standard PIMD, the value used for a bead's fictitious mass is -arbitrary. A common choice is to use Mi = m/P, which results in the -mass of the entire ring-polymer being equal to the real quantum -particle. But it can be difficult to efficiently integrate the -equations of motion for the stiff harmonic interactions in the ring -polymers. -

    -

    A useful way to resolve this issue is to integrate the equations of -motion in a normal mode representation, using Normal Mode -Path-Integral Molecular Dynamics (NMPIMD) (Cao1). In NMPIMD, -the NH chains are attached to each normal mode of the ring-polymer and -the fictitious mass of each mode is chosen as Mk = the eigenvalue of -the Kth normal mode for k > 0. The k = 0 mode, referred to as the -zero-frequency mode or centroid, corresponds to overall translation of -the ring-polymer and is assigned the mass of the real particle. -

    -

    Motion of the centroid can be effectively uncoupled from the other -normal modes by scaling the fictitious masses to achieve a partial -adiabatic separation. This is called a Centroid Molecular Dynamics -(CMD) approximation (Cao2). The time-evolution (and resulting -dynamics) of the quantum particles can be used to obtain centroid time -correlation functions, which can be further used to obtain the true -quantum correlation function for the original system. The CMD method -also uses normal modes to evolve the system, except only the k > 0 -modes are thermostatted, not the centroid degrees of freedom. -

    -

    The keyword fmass sets a further scaling factor for the fictitious -masses of beads, which can be used for the Partial Adiabatic CMD -(Hone), or to be set as P, which results in the fictitious -masses to be equal to the real particle masses. -

    -

    The keyword sp is a scaling factor on Planck's constant, which can -be useful for debugging or other purposes. The default value of 1.0 -is appropriate for most situations. -

    -

    The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme -as described in (Calhoun). In LAMMPS this is done by using -multi-replica feature in LAMMPS, where -each quasi-particle system is stored and simulated on a separate -partition of processors. The following diagram illustrates this -approach. The original system with 2 ring polymers is shown in red. -Since each ring has 4 quasi-beads (imaginary time slices), there are 4 -replicas of the system, each running on one of the 4 partitions of -processors. Each replica (shown in green) owns one quasi-bead in each -ring. -

    -
    -
    -

    To run a PIMD simulation with M quasi-beads in each ring polymer using -N MPI tasks for each partition's domain-decomposition, you would use P -= MxN processors (cores) and run the simulation as follows: -

    -
    mpirun -np P lmp_mpi -partition MxN -in script 
-
    -

    Note that in the LAMMPS input script for a multi-partition simulation, -it is often very useful to define a uloop-style -variable such as -

    -
    variable ibead uloop M pad 
-
    -

    where M is the number of quasi-beads (partitions) used in the -calculation. The uloop variable can then be used to manage I/O -related tasks for each of the partitions, e.g. -

    -
    dump dcd all dcd 10 system_${ibead}.dcd
-restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
-read_restart system_${ibead}.restart2 
-
    -

    Restrictions: -

    -

    This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    A PIMD simulation can be initialized with a single data file read via -the read_data command. However, this means all -quasi-beads in a ring polymer will have identical positions and -velocities, resulting in identical trajectories for all quasi-beads. -To avoid this, users can simply initialize velocities with different -random number seeds assigned to each partition, as defined by the -uloop variable, e.g. -

    -
    velocity all create 300.0 1234${ibead} rot yes dist gaussian 
-
    -

    Default: -

    -

    The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0, -and nhc = 2. -

    -
    - - - -

    (Feynman) R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and -Path Integrals, McGraw-Hill, New York (1965). -

    - - -

    (Tuckerman) M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993). -

    - - -

    (Cao1) J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993). -

    - - -

    (Cao2) J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994). -

    - - -

    (Hone) T. Hone, P. Rossky, G. Voth, J Chem Phys, 124, -154103 (2006). -

    - - -

    (Calhoun) A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, -415 (1996). -

    - diff --git a/doc/doc2/fix_planeforce.html b/doc/doc2/fix_planeforce.html deleted file mode 100644 index 2ef66d5a03..0000000000 --- a/doc/doc2/fix_planeforce.html +++ /dev/null @@ -1,56 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix planeforce command -

    -

    Syntax: -

    -
    fix ID group-ID planeforce x y z 
-
    -
    • ID, group-ID are documented in fix command -
    • planeforce = style name of this fix command -
    • x y z = 3-vector that is normal to the plane -
    -

    Examples: -

    -
    fix hold boundary planeforce 1.0 0.0 0.0 
-
    -

    Description: -

    -

    Adjust the forces on each atom in the group so that only the -components of force in the plane specified by the normal vector -(x,y,z) remain. This is done by subtracting out the component of -force perpendicular to the plane. -

    -

    If the initial velocity of the atom is 0.0 (or in the plane), then it -should continue to move in the plane thereafter. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix lineforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_poems.html b/doc/doc2/fix_poems.html deleted file mode 100644 index 0bc381f4e6..0000000000 --- a/doc/doc2/fix_poems.html +++ /dev/null @@ -1,146 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix poems -

    -

    Syntax: -

    -
    fix ID group-ID poems keyword values 
-
    -
    • ID, group-ID are documented in fix command - -
    • poems = style name of this fix command - -
    • keyword = group or file or molecule - -
        group values = list of group IDs
-  molecule values = none
-  file values = filename 
-
      - -
    -

    Examples: -

    -
    fix 3 fluid poems group clump1 clump2 clump3
-fix 3 fluid poems file cluster.list 
-
    -

    Description: -

    -

    Treats one or more sets of atoms as coupled rigid bodies. This means -that each timestep the total force and torque on each rigid body is -computed and the coordinates and velocities of the atoms are updated -so that the collection of bodies move as a coupled set. This can be -useful for treating a large biomolecule as a collection of connected, -coarse-grained particles. -

    -

    The coupling, associated motion constraints, and time integration is -performed by the software package Parallelizable Open source -Efficient Multibody Software (POEMS) which computes the -constrained rigid-body motion of articulated (jointed) multibody -systems (Anderson). POEMS was written and is distributed -by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, -and other members of his group at Rensselaer Polytechnic Institute -(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For -copyright information on POEMS and other details, please refer to the -documents in the poems directory distributed with LAMMPS. -

    - - -

    This fix updates the positions and velocities of the rigid atoms with -a constant-energy time integration, so you should not update the same -atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). -

    -

    Each body must have a non-degenerate inertia tensor, which means if -must contain at least 3 non-collinear atoms. Which atoms are in which -bodies can be defined via several options. -

    -

    For option group, each of the listed groups is treated as a rigid -body. Note that only atoms that are also in the fix group are -included in each rigid body. -

    -

    For option molecule, each set of atoms in the group with a different -molecule ID is treated as a rigid body. -

    -

    For option file, sets of atoms are read from the specified file and -each set is treated as a rigid body. Each line of the file specifies -a rigid body in the following format: -

    -

    ID type atom1-ID atom2-ID atom3-ID ... -

    -

    ID as an integer from 1 to M (the number of rigid bodies). Type is -any integer; it is not used by the fix poems command. The remaining -arguments are IDs of atoms in the rigid body, each typically from 1 to -N (the number of atoms in the system). Only atoms that are also in -the fix group are included in each rigid body. Blank lines and lines -that begin with '#' are skipped. -

    -

    A connection between a pair of rigid bodies is inferred if one atom is -common to both bodies. The POEMS solver treats that atom as a -spherical joint with 3 degrees of freedom. Currently, a collection of -bodies can only be connected by joints as a linear chain. The entire -collection of rigid bodies can represent one or more chains. Other -connection topologies (tree, ring) are not allowed, but will be added -later. Note that if no joints exist, it is more efficient to use the -fix rigid command to simulate the system. -

    -

    When the poems fix is defined, it will print out statistics on the -total # of clusters, bodies, joints, atoms involved. A cluster in -this context means a set of rigid bodies connected by joints. -

    -

    For computational efficiency, you should turn off pairwise and bond -interactions within each rigid body, as they no longer contribute to -the motion. The "neigh_modify exclude" and "delete_bonds" commands -can be used to do this if each rigid body is a group. -

    -

    For computational efficiency, you should only define one fix poems -which includes all the desired rigid bodies. LAMMPS will allow -multiple poems fixes to be defined, but it is more expensive. -

    -

    The degrees-of-freedom removed by coupled rigid bodies are accounted -for in temperature and pressure computations. Similarly, the rigid -body contribution to the pressure virial is also accounted for. The -latter is only correct if forces within the bodies have been turned -off, and there is only a single fix poems defined. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the POEMS package. It is only enabled if LAMMPS -was built with that package, which also requires the POEMS library be -built and linked with LAMMPS. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix rigid, delete_bonds, -neigh_modify exclude -

    -

    Default: none -

    -
    - - - -

    (Anderson) Anderson, Mukherjee, Critchley, Ziegler, and Lipton -"POEMS: Parallelizable Open-source Efficient Multibody Software ", -Engineering With Computers (2006). (link to -paper) -

    - diff --git a/doc/doc2/fix_pour.html b/doc/doc2/fix_pour.html deleted file mode 100644 index 7ce96622df..0000000000 --- a/doc/doc2/fix_pour.html +++ /dev/null @@ -1,242 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix pour command -

    -

    Syntax: -

    -
    fix ID group-ID pour N type seed keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • pour = style name of this fix command - -
    • N = # of atoms to insert - -
    • type = atom type to assign to inserted atoms (offset for molecule insertion) - -
    • seed = random # seed (positive integer) - -
    • one or more keyword/value pairs may be appended to args - -
    • keyword = region or diam or dens or vol or rate or vel or mol or rigid or shake - -
        region value = region-ID
-    region-ID = ID of region to use as insertion volume
-  diam values = dstyle args
-    dstyle = one or range or poly
-      one args = D
-        D = single diameter for inserted particles (distance units)
-      range args = Dlo Dhi
-        Dlo,Dhi = range of diameters for inserted particles (distance units)
-      poly args = Npoly D1 P1 D2 P2 ...
-        Npoly = # of (D,P) pairs
-        D1,D2,... = diameter for subset of inserted particles (distance units)
-        P1,P2,... = percentage of inserted particles with this diameter (0-1)
-  vol values = fraction Nattempt
-    fraction = desired volume fraction for filling insertion volume
-    Nattempt = max # of insertion attempts per atom
-  rate value = V
-    V = z velocity (3d) or y velocity (2d) at which
-        insertion volume moves (velocity units)
-  vel values (3d) = vxlo vxhi vylo vyhi vz
-  vel values (2d) = vxlo vxhi vy
-    vxlo,vxhi = range of x velocities for inserted particles (velocity units)
-    vylo,vyhi = range of y velocities for inserted particles (velocity units)
-    vz = z velocity (3d) assigned to inserted particles (velocity units)
-    vy = y velocity (2d) assigned to inserted particles (velocity units)
-  mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
-  molfrac values = f1 f2 ... fN
-    f1 to fN = relative probability of creating each of N molecules in template-ID
-  rigid value = fix-ID
-    fix-ID = ID of fix rigid/small command
-  shake value = fix-ID
-    fix-ID = ID of fix shake command 
-
      - -
    -

    Examples: -

    -
    fix 3 all pour 1000 2 29494 region myblock
-fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1 
-fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6
-fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid 
-
    -

    Description: -

    -

    Insert finite-size particles or molecules into the simulation box -every few timesteps within a specified region until N particles or -molecules have been inserted. This is typically used to model the -pouring of granular particles into a container under the influence of -gravity. For the remainder of this doc page, a single inserted atom -or molecule is referred to as a "particle". -

    -

    If inserted particles are individual atoms, they are assigned the -specified atom type. If they are molecules, the type of each atom in -the inserted molecule is specified in the file read by the -molecule command, and those values are added to the -specified atom type. E.g. if the file specifies atom types 1,2,3, and -those are the atom types you want for inserted molecules, then specify -type = 0. If you specify type = 2, the in the inserted molecule -will have atom types 3,4,5. -

    -

    All atoms in the inserted particle are assigned to two groups: the -default group "all" and the group specified in the fix pour command -(which can also be "all"). -

    -

    This command must use the region keyword to define an insertion -volume. The specified region must have been previously defined with a -region command. It must be of type block or a z-axis -cylinder and must be defined with side = in. The cylinder style -of region can only be used with 3d simulations. -

    -

    Individual atoms are inserted, unless the mol keyword is used. It -specifies a template-ID previously defined using the -molecule command, which reads a file that defines the -molecule. The coordinates, atom types, center-of-mass, moments of -inertia, etc, as well as any bond/angle/etc and special neighbor -information for the molecule can be specified in the molecule file. -See the molecule command for details. The only -settings required to be in this file are the coordinates and types of -atoms in the molecule. -

    -

    If the molecule template contains more than one molecule, the relative -probability of depositing each molecule can be specified by the -molfrac keyword. N relative probablities, each from 0.0 to 1.0, are -specified, where N is the number of molecules in the template. Each -time a molecule is inserted, a random number is used to sample from -the list of relative probabilities. The N values must sum to 1.0. -

    -

    If you wish to insert molecules via the mol keyword, that will be -treated as rigid bodies, use the rigid keyword, specifying as its -value the ID of a separate fix rigid/small -command which also appears in your input script. -

    -

    If you wish to insert molecules via the mol keyword, that will have -their bonds or angles constrained via SHAKE, use the shake keyword, -specifying as its value the ID of a separate fix -shake command which also appears in your input script. -

    -

    Each timestep particles are inserted, they are placed randomly inside -the insertion volume so as to mimic a stream of poured particles. If -they are molecules they are also oriented randomly. Each atom in the -particle is tested for overlaps with existing particles, including -effects due to periodic boundary conditions if applicable. If an -overlap is detected, another random insertion attempt is made; see the -vol keyword discussion below. The larger the volume of the -insertion region, the more particles that can be inserted at any one -timestep. Particles are inserted again after enough time has elapsed -that the previously inserted particles fall out of the insertion -volume under the influence of gravity. Insertions continue every so -many timesteps until the desired # of particles has been inserted. -

    -

    All other keywords are optional with defaults as shown below. -

    -

    The diam option is only used when inserting atoms and specifes the -diameters of inserted particles. There are 3 styles: one, range, -or poly. For one, all particles will have diameter D. For -range, the diameter of each particle will be chosen randomly and -uniformly between the specified Dlo and Dhi bounds. For poly, a -series of Npoly diameters is specified. For each diameter a -percentage value from 0.0 to 1.0 is also specified. The Npoly -percentages must sum to 1.0. For the example shown above with "diam 2 -0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7 -or 1.5. 40% of the particles will be small; 60% will be large. -

    -

    Note that for molecule insertion, the diameters of individual atoms in -the molecule can be specified in the file read by the -molecule command. If not specified, the diameter of -each atom in the molecule has a default diameter of 1.0. -

    -

    The dens and vel options enable inserted particles to have a range -of densities or xy velocities. The specific values for a particular -inserted particle will be chosen randomly and uniformly between the -specified bounds. The vz or vy value for option vel assigns a -z-velocity (3d) or y-velocity (2d) to each inserted particle. -

    -

    The vol option specifies what volume fraction of the insertion -volume will be filled with particles. For particles with a size -specified by the diam range keyword, they are assumed to all be of -maximum diamter Dhi for purposes of computing their contribution to -the volume fraction. -

    -

    The higher the volume fraction value, the more particles are inserted -each timestep. Since inserted particles cannot overlap, the maximum -volume fraction should be no higher than about 0.6. Each timestep -particles are inserted, LAMMPS will make up to a total of M tries to -insert the new particles without overlaps, where M = # of inserted -particles * Nattempt. If LAMMPS is unsuccessful at completing all -insertions, it prints a warning. -

    -

    The rate option moves the insertion volume in the z direction (3d) -or y direction (2d). This enables pouring particles from a -successively higher height over time. -

    -

    IMPORTANT NOTE: If you are monitoring the temperature of a system -where the particle count is changing due to adding particles, you -typically should use the compute_modify dynamic -yes command for the temperature compute you are -using. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. This means you must be careful when restarting a -pouring simulation, when the restart file was written in the middle of -the pouring operation. Specifically, you should use a new fix pour -command in the input script for the restarted simulation that -continues the operation. You will need to adjust the arguments of the -original fix pour command to do this. -

    -

    Also note that because the state of the random number generator is not -saved in restart files, you cannot do "exact" restarts with this fix, -where the simulation continues on the same as if no restart had taken -place. However, in a statistical sense, a restarted simulation should -produce the same behavior if you adjust the fix pour parameters -appropriately. -

    -

    None of the fix_modify options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various output commands. No -parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    For 3d simulations, a gravity fix in the -z direction must be defined -for use in conjunction with this fix. For 2d simulations, gravity -must be defined in the -y direction. -

    -

    The specified insertion region cannot be a "dynamic" region, as -defined by the region command. -

    -

    Related commands: -

    -

    fix_deposit, fix_gravity, -region -

    -

    Default: -

    -

    Insertions are performed for individual particles, i.e. no mol -setting is defined. If the mol keyword is used, the default for -molfrac is an equal probabilities for all molecules in the template. -Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol = -0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0. -

    - diff --git a/doc/doc2/fix_press_berendsen.html b/doc/doc2/fix_press_berendsen.html deleted file mode 100644 index 673c1b3436..0000000000 --- a/doc/doc2/fix_press_berendsen.html +++ /dev/null @@ -1,227 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix press/berendsen command -

    -

    Syntax: -

    -
    fix ID group-ID press/berendsen keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • press/berendsen = style name of this fix command - -
      one or more keyword value pairs may be appended
-keyword = iso or aniso or x or y or z or couple or dilate or modulus
-  iso or aniso values = Pstart Pstop Pdamp
-    Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
-    Pdamp = pressure damping parameter (time units)
-  x or y or z values = Pstart Pstop Pdamp
-    Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
-    Pdamp = stress damping parameter (time units)
-  couple = none or xyz or xy or yz or xz
-  modulus value = bulk modulus of system (pressure units)
-  dilate value = all or partial 
-
      - -
    -

    Examples: -

    -
    fix 1 all press/berendsen iso 0.0 0.0 1000.0
-fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial 
-
    -

    Description: -

    -

    Reset the pressure of the system by using a Berendsen barostat -(Berendsen), which rescales the system volume and -(optionally) the atoms coordinates within the simulation box every -timestep. -

    -

    Regardless of what atoms are in the fix group, a global pressure is -computed for all atoms. Similarly, when the size of the simulation -box is changed, all atoms are re-scaled to new positions, unless the -keyword dilate is specified with a value of partial, in which case -only the atoms in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of atoms in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. -

    -

    IMPORTANT NOTE: Unlike the fix npt or fix -nph commands which perform Nose/Hoover barostatting AND -time integration, this fix does NOT perform time integration. It only -modifies the box size and atom coordinates to effect barostatting. -Thus you must use a separate time integration fix, like fix -nve or fix nvt to actually update the -positions and velocities of atoms. This fix can be used in -conjunction with thermostatting fixes to control the temperature, such -as fix nvt or fix langevin or fix -temp/berendsen. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting and barostatting. -

    -
    - -

    The barostat is specified using one or more of the iso, aniso, -x, y, z, and couple keywords. These keywords give you the -ability to specify the 3 diagonal components of an external stress -tensor, and to couple various of these components together so that the -dimensions they represent are varied together during a -constant-pressure simulation. Unlike the fix npt and -fix nph commands, this fix cannot be used with triclinic -(non-orthogonal) simulation boxes to control all 6 components of the -general pressure tensor. -

    -

    The target pressures for each of the 3 diagonal components of the -stress tensor can be specified independently via the x, y, z, -keywords, which correspond to the 3 simulation box dimensions. For -each component, the external pressure or tensor component at each -timestep is a ramped value during the run from Pstart to Pstop. -If a target pressure is specified for a component, then the -corresponding box dimension will change during a simulation. For -example, if the y keyword is used, the y-box length will change. A -box dimension will not change if that component is not specified, -although you have the option to change that dimension via the fix -deform command. -

    -

    For all barostat keywords, the Pdamp parameter determines the time -scale on which pressure is relaxed. For example, a value of 1000.0 -means to relax the pressure in a timespan of (roughly) 1000 time units -(tau or fmsec or psec - see the units command). -

    -

    IMPORTANT NOTE: The relaxation time is actually also a function of the -bulk modulus of the system (inverse of isothermal compressibility). -The bulk modulus has units of pressure and is the amount of pressure -that would need to be applied (isotropically) to reduce the volume of -the system by a factor of 2 (assuming the bulk modulus was a constant, -independent of density, which it's not). The bulk modulus can be set -via the keyword modulus. The Pdamp parameter is effectively -multiplied by the bulk modulus, so if the pressure is relaxing faster -than expected or desired, increasing the bulk modulus has the same -effect as increasing Pdamp. The converse is also true. LAMMPS does -not attempt to guess a correct value of the bulk modulus; it just uses -10.0 as a default value which gives reasonable relaxation for a -Lennard-Jones liquid, but will be way off for other materials and way -too small for solids. Thus you should experiment to find appropriate -values of Pdamp and/or the modulus when using this fix. -

    -
    - -

    The couple keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, xz -means the Pxx and Pzz components of the stress tensor are coupled. -Xyz means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -Pstart, Pstop, Pdamp parameters for any coupled dimensions must -be identical. Couple xyz can be used for a 2d simulation; the z -dimension is simply ignored. -

    -
    - -

    The iso and aniso keywords are simply shortcuts that are -equivalent to specifying several other keywords together. -

    -

    The keyword iso means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Pstart Pstop Pdamp" is the same as -specifying these 4 keywords: -

    -
    x Pstart Pstop Pdamp
-y Pstart Pstop Pdamp
-z Pstart Pstop Pdamp
-couple xyz 
-
    -

    The keyword aniso means x, y, and z dimensions are controlled -independently using the Pxx, Pyy, and Pzz components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying -these 4 keywords: -

    -
    x Pstart Pstop Pdamp
-y Pstart Pstop Pdamp
-z Pstart Pstop Pdamp
-couple none 
-
    -
    - -

    This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if these commands had been issued: -

    -
    compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp 
-
    -

    See the compute temp and compute -pressure commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is the same -as the fix group. -

    -

    Note that these are NOT the computes used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp -and thermo_press. This means you can change the attributes of this -fix's temperature or pressure via the -compute_modify command or print this temperature -or pressure during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify temp and press options are -supported by this fix. You can use them to assign a -compute you have defined to this fix which will be used -in its temperature and pressure calculations. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. -

    -

    No global or per-atom quantities are stored by this fix for access by -various output commands. -

    -

    This fix can ramp its target pressure over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    Any dimension being adjusted by this fix must be periodic. -

    -

    Related commands: -

    -

    fix nve, fix nph, fix -npt, fix temp/berendsen, -fix_modify -

    -

    Default: -

    -

    The keyword defaults are dilate = all, modulus = 10.0 in units of -pressure for whatever units are defined. -

    -
    - - - -

    (Berendsen) Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem -Phys, 81, 3684 (1984). -

    - diff --git a/doc/doc2/fix_print.html b/doc/doc2/fix_print.html deleted file mode 100644 index 245735dac5..0000000000 --- a/doc/doc2/fix_print.html +++ /dev/null @@ -1,102 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix print command -

    -

    Syntax: -

    -
    fix ID group-ID print N string keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • print = style name of this fix command - -
    • N = print every N steps - -
    • string = text string to print with optional variable names - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = file or append or screen or title - -
        file value = filename
-  append value = filename
-  screen value = yes or no
-  title value = string
-    string =  text to print as 1st line of output file 
-
      - -
    -

    Examples: -

    -
    fix extra all print 100 "Coords of marker atom = $x $y $z"
-fix extra all print 100 "Coords of marker atom = $x $y $z" file coord.txt 
-
    -

    Description: -

    -

    Print a text string every N steps during a simulation run. This can -be used for diagnostic purposes or as a debugging tool to monitor some -quantity during a run. The text string must be a single argument, so -it should be enclosed in double quotes if it is more than one word. -If it contains variables it must be enclosed in double quotes to -insure they are not evaluated when the input script line is read, but -will instead be evaluated each time the string is printed. -

    -

    The specified group-ID is ignored by this fix. -

    -

    See the variable command for a description of equal -style variables which are the most useful ones to use with the fix -print command, since they are evaluated afresh each timestep that the -fix print line is output. Equal-style variables calculate formulas -involving mathematical operations, atom properties, group properties, -thermodynamic properties, global values calculated by a -compute or fix, or references to other -variables. -

    -

    If the file or append keyword is used, a filename is specified to -which the output generated by this fix will be written. If file is -used, then the filename is overwritten if it already exists. If -append is used, then the filename is appended to if it already -exists, or created if it does not exist. -

    -

    If the screen keyword is used, output by this fix to the screen and -logfile can be turned on or off as desired. -

    -

    The title keyword allow specification of the string that will be -printed as the first line of the output file, assuming the file -keyword was used. By default, the title line is as follows: -

    -
    # Fix print output for fix ID 
-
    -

    where ID is replaced with the fix-ID. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    variable, print -

    -

    Default: -

    -

    The option defaults are no file output, screen = yes, and title string -as described above. -

    - diff --git a/doc/doc2/fix_property_atom.html b/doc/doc2/fix_property_atom.html deleted file mode 100644 index c17eb032c2..0000000000 --- a/doc/doc2/fix_property_atom.html +++ /dev/null @@ -1,226 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix property/atom command -

    -

    Syntax: -

    -
    fix ID group-ID property/atom vec1 vec2 ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • property/atom = style name of this fix command - -
    • vec1,vec2,... = mol or q or i_name or d_name - -
        mol = molecule IDs
-  q = charge
-  i_name = new integer vector referenced by name
-  d_name = new floating-point vector referenced by name 
-
      -
    • zero of more keyword/value pairs may be appended - -
    • keyword = ghost - -
        ghost value = no or yes for whether ghost atom info in communicated 
-
      - -
    -

    Examples: -

    -
    fix 1 all property/atom mol
-fix 1 all property/atom i_myflag1 i_myflag2
-fix 1 all property/atom d_sx d_sy d_sz 
-
    -

    Description: -

    -

    Create one or more additional per-atom vectors to store information -about atoms and to use during a simulation. The specified group-ID -is ignored by this fix. -

    -

    The atom style used for a simulation defines a set of per-atom -properties, as explained on the atom_style and -read_data doc pages. The latter command allows these -properties to be defined for each atom in the system when a data file -is read. This fix will augment the set of properties with new custom -ones. -

    -

    This can be useful in at least two scenarios. -

    -

    If the atom style does not define molecule IDs or per-atom charge, -they can be added using the mol or q keywords. This can be -useful, e.g, to define "molecules" to use as rigid bodies with the -fix rigid command, or just to carry around an extra -flag with the atoms (stored as a molecule ID). An alternative is to -use an atom style that does define molecule IDs or charge or to use a -hybrid atom style that combines two styles to allow for molecule IDs -or charge, but that has 2 practical drawbacks. First it typically -necessitates changing the format of the data file. And it may define -additional properties that aren't needed such as bond lists, which has -some overhead when there are no bonds. -

    -

    In the future, we may add additional per-atom properties similar to -mol or q, which "turn-on" specific properties defined by some atom -styles, so they can be used by atom styles that don't define them. -

    -

    More generally, the i_name and d_name vectors allow one or more -new custom per-atom properties to be defined. Each name must be -unique and can use alphanumeric or underscore characters. These -vectors can store whatever values you decide are useful in your -simulation. As explained below there are several ways to initialize -and access and output these values, both via input script commands and -in new code that you add to LAMMPS. -

    -

    This is effectively a simple way to add per-atom properties to a model -without needing to write code for a new atom style -that defines the properties. Note however that implementing a new -atom style allows new atom properties to be more tightly and -seamlessly integrated with the rest of the code. -

    -

    The new atom properties encode values that migrate with atoms to new -processors and are written to restart files. If you want the new -properties to also be defined for ghost atoms, then use the ghost -keyword with a value of yes. This will invoke extra communication -when ghost atoms are created (at every re-neighboring) to insure the -new properties are also defined for the ghost atoms. -

    -

    IMPORTANT NOTE: If you use this command with the mol or charge -vectors than you most likely want to set ghost yes, since these -properties are stored with ghost atoms if you use an -atom_style that defines them, and many LAMMPS -operations that use molecule IDs or charge, such as neighbor lists and -pair styles, will expect ghost atoms to have these valuse. LAMMPS -will issue a warning it you define those vectors but do not set -ghost yes. -

    -

    IMPORTANT NOTE: The properties for ghost atoms are not updated every -timestep, but only once every few steps when neighbor lists are -re-built. Thus the ghost keyword is suitable for static properties, -like molecule IDs, but not for dynamic properties that change every -step. For the latter, the code you add to LAMMPS to change the -properties will also need to communicate their new values to/from -ghost atoms, an operation that can be invoked from within a pair -style or fix or compute -that you write. -

    -
    - -

    This fix is one of a small number that can be defined in an input -script before the simulation box is created or atoms are defined. -This is so it can be used with the read_data command -as described below. -

    -

    Per-atom properties that are defined by the atom -style are initialized when atoms are created, e.g. by -the read_data or create_atoms -commands. The per-atom properaties defined by this fix are not. So -you need to initialize them explicitly. This can be done by the -read_data command, using its fix keyword and -passing it the fix-ID of this fix. -

    -

    Thus these commands: -

    -
    fix prop all property/atom mol d_flag
-read_data data.txt fix prop NULL Molecules 
-
    -

    would allow a data file to have a section like this: -

    -
    Molecules 
-
    -
    1 4 1.5
-2 4 3.0
-3 10 1.0
-4 10 1.0
-5 10 1.0
-...
-N 763 4.5 
-
    -

    where N is the number of atoms, and the first field on each line is -the atom-ID, followed by a molecule-ID and a floating point value that -will be stored in a new property called "flag". Note that the list of -per-atom properties can be in any order. -

    -

    Another way of initializing the new properties is via the -set command. For example, if you wanted molecules -defined for every set of 10 atoms, based on their atom-IDs, -these commands could be used: -

    -
    fix prop all property/atom mol
-variable cluster atom ((id-1)/10)+1
-set id * mol v_cluster 
-
    -

    The atom-style variable will create values for atoms -with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the -set commands assigns them to the molecule ID for each atom, -they will be truncated to an integer value, so atoms 31-40 will all be -assigned a molecule ID of 4. -

    -

    Note that atomfile-style variables can also be used in -place of atom-style variables, which means in this case that the -molecule IDs could be read-in from a separate file and assinged by the -set command. This allows you to initialize new per-atom -properties in a completely general fashion. -

    -
    - -

    For new atom properties specified as i_name or d_name, the -compute property/atom command can access -their values. This means that the values can be output via the dump -custom command, accessed by fixes like fix -ave/atom, accessed by other computes like compute -reduce, or used in atom-style -variables. -

    -

    For example, these commands will output two new properties to a custom -dump file: -

    -
    fix prop all property/atom i_flag1 d_flag2
-compute 1 all property/atom i_flag1 d_flag2
-dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] 
-
    -
    - -

    If you wish to add new pair styles, -fixes, or computes that use the per-atom -properties defined by this fix, see Section -modify of the manual which has some details -on how the properties can be accessed from added classes. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the per-atom values it stores to binary restart -files, so that the values can be restored when a -simulation is restarted. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    read_data, set, compute -property/atom -

    -

    Default: -

    -

    The default keyword values are ghost = no. -

    - diff --git a/doc/doc2/fix_qbmsst.html b/doc/doc2/fix_qbmsst.html deleted file mode 100644 index 376c73eed0..0000000000 --- a/doc/doc2/fix_qbmsst.html +++ /dev/null @@ -1,232 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix qbmsst command -

    -

    Syntax: -

    -
    fix ID group-ID qbmsst dir shockvel keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • qbmsst = style name of this fix - -
    • dir = x or y or z - -
    • shockvel = shock velocity (strictly positive, velocity units) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = q or mu or p0 or v0 or e0 or tscale or damp or seedor f_max or N_f or eta or beta or T_init - -
        q value = cell mass-like parameter (mass^2/distance^4 units)
-  mu value = artificial viscosity (mass/distance/time units)
-  p0 value = initial pressure in the shock equations (pressure units)
-  v0 value = initial simulation cell volume in the shock equations (distance^3 units)
-  e0 value = initial total energy (energy units)
-  tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
-  damp value = damping parameter (time units) inverse of friction γ
-  seed value = random number seed (positive integer)
-  f_max value = upper cutoff frequency of the vibration spectrum (1/time units)
-  N_f value = number of frequency bins (positive integer)
-  eta value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
-  beta value = the quantum temperature is updated every beta time steps (positive integer)
-  T_init value = quantum temperature for the initial state (temperature units) 
-
      - -
    -

    Examples: -

    -
    fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
-fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) 
-
    -

    Two example input scripts are given, including shocked alpha quartz -and shocked liquid methane. The input script first equilibrate an -initial state with the quantum thermal bath at the target temperature -and then apply the qbmsst to simulate shock compression with quantum -nuclear correction. The following two figures plot related quantities -for shocked alpha quartz. -

    -
    -
    -

    Figure 1. Classical temperature Tcl = ∑ -mivi2/3NkB vs. time -for coupling the alpha quartz initial state with the quantum thermal -bath at target quantum temperature Tqm = 300 K. The -NpH ensemble is used for time integration while QTB provides the -colored random force. Tcl converges at the timescale -of damp which is set to be 1 ps. -

    -
    -
    -

    Figure 2. Quantum temperature and pressure vs. time for simulating -shocked alpha quartz with the QBMSST. The shock propagates along the z -direction. Restart of the QBMSST command is demonstrated in the -example input script. Thermodynamic quantities stay continuous before -and after the restart. -

    -

    Description: -

    -

    This command performs the Quantum-Bath coupled Multi-Scale Shock -Technique (QBMSST) integration. See (Qi) for a detailed -description of this method. The QBMSST provides description of the -thermodynamics and kinetics of shock processes while incorporating -quantum nuclear effects. The shockvel setting determines the steady -shock velocity that will be simulated along direction dir. -

    -

    Quantum nuclear effects (fix qtb) can be crucial -especially when the temperature of the initial state is below the -classical limit or there is a great change in the zero point energies -between the initial and final states. Theoretical post processing -quantum corrections of shock compressed water and methane have been -reported as much as 30% of the temperatures (Goldman). A -self-consistent method that couples the shock to a quantum thermal -bath described by a colored noise Langevin thermostat has been -developed by Qi et al (Qi) and applied to shocked methane. The -onset of chemistry is reported to be at a pressure on the shock -Hugoniot that is 40% lower than observed with classical molecular -dynamics. -

    -

    It is highly recommended that the system be already in an equilibrium -state with a quantum thermal bath at temperature of T_init. The fix -command fix qtb at constant temperature T_init could -be used before applying this command to introduce self-consistent -quantum nuclear effects into the initial state. -

    -

    The parameters q, mu, e0, p0, v0 and tscale are described -in the command fix msst. The values of e0, p0, or -v0 will be calculated on the first step if not specified. The -parameter of damp, f_max, and N_f are described in the command -fix qtb. -

    -

    The fix qbmsst command couples the shock system to a quantum thermal -bath with a rate that is proportional to the change of the total -energy of the shock system, etot - etot0. -Here etot consists of both the system energy and a thermal -term, see (Qi), and etot0 = e0 is the -initial total energy. -

    -

    The eta (η) parameter is a unitless coupling constant -between the shock system and the quantum thermal bath. A small eta -value cannot adjust the quantum temperature fast enough during the -temperature ramping period of shock compression while large eta -leads to big temperature oscillation. A value of eta between 0.3 and -1 is usually appropriate for simulating most systems under shock -compression. We observe that different values of eta lead to almost -the same final thermodynamic state behind the shock, as expected. -

    -

    The quantum temperature is updated every beta (β) steps -with an integration time interval beta times longer than the -simulation time step. In that case, etot is taken as its -average over the past beta steps. The temperature of the quantum -thermal bath Tqm changes dynamically according to -the following equation where Δt is the MD time step and -γ is the friction constant which is equal to the inverse -of the damp parameter. -

    -
    dTqm/dt = -γη∑βl = -1[etot(t-lΔt)-etot0]/3βNkB -
    - -

    The parameter T_init is the initial temperature of the quantum -thermal bath and the system before shock loading. -

    -

    For all pressure styles, the simulation box stays orthorhombic in -shape. Parrinello-Rahman boundary conditions (tilted box) are -supported by LAMMPS, but are not implemented for QBMSST. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Because the state of the random number generator is not written to -binary restart files, this fix cannot be restarted -"exactly" in an uninterrupted fashion. However, in a statistical -sense, a restarted simulation should produce similar behaviors of the -system as if it is not interrupted. To achieve such a restart, one -should write explicitly the same value for q, mu, damp, f_max, -N_f, eta, and beta and set tscale = 0 if the system is -compressed during the first run. -

    -

    The progress of the QBMSST can be monitored by printing the global -scalar and global vector quantities computed by the fix. The global -vector contains five values in this order: -

    -

    [dhugoniot, drayleigh, lagrangian_speed, lagrangian_position, -quantum_temperature] -

    -
    1. dhugoniot is the departure from the Hugoniot (temperature units). -
    2. drayleigh is the departure from the Rayleigh line (pressure units). -
    3. lagrangian_speed is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). -
    4. lagrangian_position is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front. -
    5. quantum_temperature is the temperature of the quantum thermal bath Tqm. -
    -

    To print these quantities to the log file with descriptive column -headers, the following LAMMPS commands are suggested. Here the -fix_modify energy command is also enabled to allow -the thermo keyword etotal to print the quantity etot. See -also the thermo_style command. -

    -
    fix		fix_id all msst z 
-fix_modify	fix_id energy yes
-variable	dhug	equal f_fix_id[1]
-variable	dray	equal f_fix_id[2]
-variable	lgr_vel	equal f_fix_id[3]
-variable	lgr_pos	equal f_fix_id[4]
-variable	T_qm	equal f_fix_id[5]
-thermo_style	custom	step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id 
-
    -

    The global scalar under the entry f_fix_id is the quantity of thermo -energy as an extra part of etot. This global scalar and the -vector of 5 quantities can be accessed by various output -commands. It is worth noting that the -temp keyword under the thermo_style command print -the instantaneous classical temperature Tcl as -described in the command fix qtb. -

    -
    - -

    Restrictions: -

    -

    This fix style is part of the USER-QTB package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    All cell dimensions must be periodic. This fix can not be used with a -triclinic cell. The QBMSST fix has been tested only for the group-ID -all. -

    -
    - -

    Related commands: -

    -

    fix qtb, fix msst -

    -
    - -

    Default: -

    -

    The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed -= 880302, f_max = 200.0, N_f = 100, eta = 1.0, beta = 100, and -T_init=300.0. e0, p0, and v0 are calculated on the first step. -

    -
    - - - -

    (Goldman) Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009) -

    - - -

    (Qi) Qi and Reed, J. Phys. Chem. A 116, 10451 (2012). -

    - diff --git a/doc/doc2/fix_qeq.html b/doc/doc2/fix_qeq.html deleted file mode 100644 index e4abfa5316..0000000000 --- a/doc/doc2/fix_qeq.html +++ /dev/null @@ -1,209 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix qeq/point command -

    -

    fix qeq/shielded command -

    -

    fix qeq/slater command -

    -

    fix qeq/dynamic command -

    -

    Syntax: -

    -
    fix ID group-ID style Nevery cutoff tolerance maxiter qfile 
-
    -
    • ID, group-ID are documented in fix command -
    • style = qeq/point or qeq/shielded or qeq/slater or qeq/dynamic -
    • Nevery = perform charge equilibration every this many steps -
    • cutoff = global cutoff for charge-charge interactions (distance unit) -
    • tolerance = precision to which charges will be equilibrated -
    • maxiter = maximum iterations to perform charge equilibration -
    • qfile = a filename with QEq parameters -
    -

    Examples: -

    -
    fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
-fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
-fix 1 all qeq/slater 5 10 1.0e-6 100 params
-fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq 
-
    -

    Description: -

    -

    Perform the charge equilibration (QEq) method as described in (Rappe -and Goddard) and formulated in (Nakano) (also known -as the matrix inversion method) and in (Rick and Stuart) (also -known as the extended Lagrangian method) based on the -electronegativity equilization principle. -

    -

    These fixes can be used with any pair style in -LAMMPS, so long as per-atom charges are defined. The most typical -use-case is in conjunction with a pair style that -performs charge equilibration periodically (e.g. every timestep), such -as the ReaxFF or Streitz-Mintmire potential (the latter is not yet -implemented in LAMMPS). But these fixes can also be used with -potentials that normally assume per-atom charges are fixed, e.g. a -Buckingham or LJ/Coulombic potential. -

    -

    Because the charge equilibration calculation is effectively -independent of the pair style, these fixes can also be used to perform -a one-time assignment of charges to atoms. For example, you could -define the QEq fix, perform a zero-timestep run via the run -command without any pair style defined which would set per-atom -charges (based on the current atom configuration), then remove the fix -via the unfix command before performing further dynamics. -

    -

    IMPORTANT NOTE: Computing and using charge values different from -published values defined for a fixed-charge potential like Buckingham -or CHARMM or AMBER, can have a strong effect on energies and forces, -and produces a different model than the published versions. -

    -

    IMPORTANT NOTE: The fix qeq/comb command must -still be used to perform charge equliibration with the COMB -potential. The fix qeq/reax -command can be used to perform charge equilibration with the ReaxFF -force field, although fix qeq/shielded yields the -same results as fix qeq/reax if Nevery, cutoff, and tolerance are -the same. Eventually the fix qeq/reax command will be deprecated. -

    -

    The QEq method minimizes the electrostatic energy of the system (or -equalizes the derivative of energy with respect to charge of all the -atoms) by adjusting the partial charge on individual atoms based on -interactions with their neighbors within cutoff. It reqires a few -parameters, in metal units, for each atom type which provided in a -file specified by qfile. The file has the following format -

    -
    1 chi eta gamma zeta qcore
-2 chi eta gamma zeta qcore
-...
-Ntype chi eta gamma zeta qcore 
-
    -

    There is one line per atom type with the following parameters. -Only a subset of the parameters is used by each QEq style as descibed -below, thus the others can be set to 0.0 if desired. -

    -
    • chi = electronegativity in energy units -
    • eta = self-Coulomb potential in energy units -
    • gamma = shielded Coulomb constant defined by ReaxFF force field in distance units -
    • zeta = Slater type orbital exponent defined by the Streitz-Mintmire potential in reverse distance units -
    • qcore = charge of the nucleus defined by the Streitz-Mintmire potential potential in charge units -
    -

    The qeq/point style describes partial charges on atoms as point -charges. Interaction between a pair of charged particles is 1/r, -which is the simplest description of the interaction between charges. -Only the chi and eta parameters from the qfile file are used. -Note that Coulomb catastrophe can occur if repulsion between the pair -of charged particles is too weak. This style solves partial charges -on atoms via the matrix inversion method. A tolerance of 1.0e-6 is -usually a good number. -

    -

    The qeq/shielded style describes partial charges on atoms also as -point charges, but uses a shielded Coulomb potential to describe the -interaction between a pair of charged particles. Interaction through -the shielded Coulomb is given by equation (13) of the ReaxFF force -field paper. The shielding accounts for charge overlap -between charged particles at small separation. This style is the same -as fix qeq/reax, and can be used with pair_style -reax/c. Only the chi, eta, and gamma -parameters from the qfile file are used. This style solves partial -charges on atoms via the matrix inversion method. A tolerance of -1.0e-6 is usually a good number. -

    -

    The qeq/slater style describes partial charges on atoms as spherical -charge densities centered around atoms via the Slater 1s orbital, so -that the interaction between a pair of charged particles is the -product of two Slater 1s orbitals. The expression for the Slater -1s orbital is given under equation (6) of the -Streitz-Mintmire paper. Only the chi, eta, zeta, and -qcore parameters from the qfile file are used. This style solves -partial charges on atoms via the matrix inversion method. A tolerance -of 1.0e-6 is usually a good number. -

    -

    The qeq/dynamic style describes partial charges on atoms as point -charges that interact through 1/r, but the extended Lagrangian method -is used to solve partial charges on atoms. Only the chi and eta -parameters from the qfile file are used. Note that Coulomb -catastrophe can occur if repulsion between the pair of charged -particles is too weak. A tolerance of 1.0e-3 is usually a good -number. -

    -

    Note that qeq/point, qeq/shielded, and qeq/slater describe -different charge models, whereas the matrix inversion method and the -extended Lagrangian method (qeq/dynamic) are different solvers. -

    -

    Note that the qeq/point and the qeq/dynamic styles both describe -charges as point charges that interact through 1/r relationship, but -solve partial charges on atoms using different solvers. Styles -qeq/point and the qeq/dynamic should yield comparable results if -the QEq parameters and Nevery, cutoff, and tolerance are the -same. Style qeq/point is typically faster, but qeq/dynamic scales -better on larger sizes. -

    -

    IMPORTANT NOTE: To avoid the evaluation of the derivative of charge -with respect to position, which is typically ill-defined, the system -should have a zero net charge. -

    -

    IMPORTANT NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and -qcore) is an "art". Charges on atoms are not guaranteed to -equilibrate with arbitrary choices of these parameters. We do not -develop these QEq paramters. See the examples/qeq directory for some -examples. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about these fixes is written to binary restart -files. No global scalar or vector or per-atom -quantities are stored by these fixes for access by various output -commands. No parameter of these fixes -can be used with the start/stop keywords of the run -command. -

    -

    Thexe fixes are invoked during energy minimization. -

    -

    Restrictions: -

    -

    These fixes are part of the QEQ package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix qeq/reax, fix qeq/comb -

    -

    Default: none -

    -
    - - - -

    (Rappe and Goddard) A. K. Rappe and W. A. Goddard III, J Physical -Chemistry, 95, 3358-3363 (1991). -

    - - -

    (Nakano) A. Nakano, Computer Physics Communications, 104, 59-69 (1997). -

    - - -

    (Rick and Stuart) S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics -101, 16141 (1994). -

    - - -

    (Streitz-Mintmire) F. H. Streitz, J. W. Mintmire, Physical Review B, 50, -16, 11996 (1994) -

    - - -

    (ReaxFF) A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J -Physical Chemistry, 105, 9396-9049 (2001) -

    - diff --git a/doc/doc2/fix_qeq_comb.html b/doc/doc2/fix_qeq_comb.html deleted file mode 100644 index 4ae321f0f2..0000000000 --- a/doc/doc2/fix_qeq_comb.html +++ /dev/null @@ -1,145 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix qeq/comb command -

    -

    fix qeq/comb/omp command -

    -

    Syntax: -

    -
    fix ID group-ID qeq/comb Nevery precision keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • qeq/comb = style name of this fix command - -
    • Nevery = perform charge equilibration every this many steps - -
    • precision = convergence criterion for charge equilibration - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = file - -
        file value = filename
-    filename = name of file to write QEQ equilibration info to 
-
      - -
    -

    Examples: -

    -
    fix 1 surface qeq/comb 10 0.0001 
-
    -

    Description: -

    -

    Perform charge equilibration (QeQ) in conjunction with the COMB -(Charge-Optimized Many-Body) potential as described in -(COMB_1) and (COMB_2). It performs the charge -equilibration portion of the calculation using the so-called QEq -method, whereby the charge on each atom is adjusted to minimize the -energy of the system. This fix can only be used with the COMB -potential; see the fix qeq/reax command for a QeQ -calculation that can be used with any potential. -

    -

    Only charges on the atoms in the specified group are equilibrated. -The fix relies on the pair style (COMB in this case) to calculate the -per-atom electronegativity (effective force on the charges). An -electronegativity equalization calculation (or QEq) is performed in an -interative fashion, which in parallel requires communication at each -iteration for processors to exchange charge information about nearby -atoms with each other. See Rappe_and_Goddard and -Rick_and_Stuart for details. -

    -

    During a run, charge equilibration is peformed every Nevery time -steps. Charge equilibration is also always enforced on the first step -of each run. The precision argument controls the tolerance for the -difference in electronegativity for all atoms during charge -equilibration. Precision is a trade-off between the cost of -performing charge equilibration (more iterations) and accuracy. -

    -

    If the file keyword is used, then information about each -equilibration calculation is written to the specifed file. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix produces a per-atom vector which can be accessed by various -output commands. The vector stores the -gradient of the charge on each atom. The per-atom values be accessed -on any timestep. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    This fix can be invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix command currently only supports pair style comb. -

    -

    Related commands: -

    -

    pair_style comb -

    -

    Default: -

    -

    No file output is performed. -

    -
    - - - -

    (COMB_1) J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), -

    - - -

    (COMB_2) T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R. -Phillpot, Phys Rev B, 81, 125328 (2010). -

    - - -

    (Rappe_and_Goddard) A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 -(1991). -

    - - -

    (Rick_and_Stuart) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys -101, 16141 (1994). -

    - diff --git a/doc/doc2/fix_qeq_reax.html b/doc/doc2/fix_qeq_reax.html deleted file mode 100644 index 79f8340d5c..0000000000 --- a/doc/doc2/fix_qeq_reax.html +++ /dev/null @@ -1,106 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix qeq/reax command -

    -

    Syntax: -

    -
    fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params 
-
    -
    • ID, group-ID are documented in fix command -
    • qeq/reax = style name of this fix command -
    • Nevery = perform QEq every this many steps -
    • cutlo,cuthi = lo and hi cutoff for Taper radius -
    • tolerance = precision to which charges will be equilibrated -
    • params = reax/c or a filename -
    -

    Examples: -

    -
    fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
-fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq 
-
    -

    Description: -

    -

    Perform the charge equilibration (QEq) method as described in (Rappe -and Goddard) and formulated in (Nakano). It is -typically used in conjunction with the ReaxFF force field model as -implemented in the pair_style reax/c command, but -it can be used with any potential in LAMMPS, so long as it defines and -uses charges on each atom. The fix qeq/comb -command should be used to perform charge equliibration with the COMB -potential. For more technical details about the -charge equilibration performed by fix qeq/reax, see the -(Aktulga) paper. -

    -

    The QEq method minimizes the electrostatic energy of the system by -adjusting the partial charge on individual atoms based on interactions -with their neighbors. It reqires some parameters for each atom type. -If the params setting above is the word "reax/c", then these are -extracted from the pair_style reax/c command and -the ReaxFF force field file it reads in. If a file name is specified -for params, then the parameters are taken from the specified file -and the file must contain one line for each atom type. The latter -form must be used when performing QeQ with a non-ReaxFF potential. -Each line should be formatted as follows: -

    -
    itype chi eta gamma 
-
    -

    where itype is the atom type from 1 to Ntypes, chi denotes the -electronegativity in eV, eta denotes the self-Coulomb -potential in eV, and gamma denotes the valence orbital -exponent. Note that these 3 quantities are also in the ReaxFF -potential file, except that eta is defined here as twice the eta value -in the ReaxFF file. Note that unlike the rest of LAMMPS, the units -of this fix are hard-coded to be A, eV, and electronic charge. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. No global scalar or vector or per-atom -quantities are stored by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -

    -

    This fix is invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-REAXC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix does not correctly handle interactions -involving multiple periodic images of the same atom. Hence, it should not -be used for periodic cell dimensions less than 10 angstroms. -

    -

    Related commands: -

    -

    pair_style reax/c -

    -

    Default: none -

    -
    - - - -

    (Rappe) Rappe and Goddard III, Journal of Physical Chemistry, 95, -3358-3363 (1991). -

    - - -

    (Nakano) Nakano, Computer Physics Communications, 104, 59-69 (1997). -

    - - -

    (Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, -245-259 (2012). -

    - diff --git a/doc/doc2/fix_qmmm.html b/doc/doc2/fix_qmmm.html deleted file mode 100644 index d10da4e27c..0000000000 --- a/doc/doc2/fix_qmmm.html +++ /dev/null @@ -1,71 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix qmmm command -

    -

    Syntax: -

    -
    fix ID group-ID qmmm  
-
    -
    • ID, group-ID are documented in fix command -
    • qmmm = style name of this fix command -
    -

    Examples: -

    -

    fix 1 qmol qmmm -

    -

    Description: -

    -

    This fix provides functionality to enable a quantum -mechanics/molecular mechanice (QM/MM) coupling of LAMMPS to a quantum -mechanical code. The current implementation only supports an ONIOM -style mechanical coupling to the Quantum ESPRESSO plane -wave DFT package. Electrostatic coupling is in preparation and the -interface has been written in a manner that coupling to other QM codes -should be possible without changes to LAMMPS itself. -

    - - -

    The interface code for this is in the lib/qmmm directory of the LAMMPS -distribution and is being made available at this early stage of -development in order to encourage contributions for interfaces to -other QM codes. This will allow the LAMMPS side of the implementation -to be adapted if necessary before being finalized. -

    -

    Details about how to use this fix are currently documented in the -description of the QM/MM interface code itself in lib/qmmm/README. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-QMMM package. It is only enabled if -LAMMPS was built with that package. It also requires building a -library provided with LAMMPS. See the Making -LAMMPS section for more info. -

    -

    The fix is only functional when LAMMPS is built as a library and -linked with a compatible QM program and a QM/MM frontend into a QM/MM -executable. See the lib/qmmm/README file for details. -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_qtb.html b/doc/doc2/fix_qtb.html deleted file mode 100644 index 45333c0bc2..0000000000 --- a/doc/doc2/fix_qtb.html +++ /dev/null @@ -1,194 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix qtb command -

    -

    Syntax: -

    -
    fix ID group-ID qtb keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • qtb = style name of this fix - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = temp or damp or seed or f_max or N_f - -
        temp value = target quantum temperature (temperature units)
-  damp value = damping parameter (time units) inverse of friction &gamma;
-  seed value = random number seed (positive integer)
-  f_max value = upper cutoff frequency of the vibration spectrum (1/time units)  
-  N_f value = number of frequency bins (positive integer) 
-
      - -
    -

    Examples: -

    -
    fix 1 all nve
-fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
-fix 2 all nph iso 1.01325 1.01325 1
-fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units) 
-
    -

    Description: -

    -

    This command performs the quantum thermal bath scheme proposed by -(Dammak) to include self-consistent quantum nuclear effects, -when used in conjunction with the fix nve or fix -nph commands. -

    -

    Classical molecular dynamics simulation does not include any quantum -nuclear effect. Quantum treatment of the vibrational modes will -introduce zero point energy into the system, alter the energy power -spectrum and bias the heat capacity from the classical limit. Missing -all the quantum nuclear effects, classical MD cannot model systems at -temperatures lower than their classical limits. This effect is -especially important for materials with a large population of hydrogen -atoms and thus higher classical limits. -

    -

    The equation of motion implemented by this command follows a Langevin -form: -

    -
    miai = fi -+ Ri - -miγvi.
    - -

    Here mi, ai, fi -, Ri, γ and vi -represent mass, acceleration, force exerted by all other atoms, random -force, frictional coefficient (the inverse of damping parameter damp), -and velocity. The random force Ri is "colored" so -that any vibrational mode with frequency ω will have a -temperature-sensitive energy θ(ω,T) which -resembles the energy expectation for a quantum harmonic oscillator -with the same natural frequency: -

    -
    θ(ω,T) = -ℏω/2 + -ℏω[exp(ℏω/kBT)-1]-1 -
    - -

    To efficiently generate the random forces, we employ the method -of (Barrat), that circumvents the need to generate all -random forces for all times before the simulation. The memory -requirement of this approach is less demanding and independent -of the simulation duration. Since the total random force Rtot -does not necessarily vanish for a finite number of atoms, -Ri is replaced by Ri - Rtot/Ntot -to avoid collective motion of the system. -

    -

    The temp parameter sets the target quantum temperature. LAMMPS will -still have an output temperature in its thermo style. That is the -instantaneous classical temperature Tcl derived from -the atom velocities at thermal equilibrium. A non-zero -Tcl will be present even when the quantum -temperature approaches zero. This is associated with zero-point energy -at low temperatures. -

    -
    Tcl = ∑ -mivi2/3NkB -
    - -

    The damp parameter is specified in time units, and it equals the -inverse of the frictional coefficient γ. γ -should be as small as possible but slightly larger than the timescale -of anharmonic coupling in the system which is about 10 ps to 100 -ps. When γ is too large, it gives an energy spectrum that -differs from the desired Bose-Einstein spectrum. When γ -is too small, the quantum thermal bath coupling to the system will be -less significant than anharmonic effects, reducing to a classical -limit. We find that setting γ between 5 THz and 1 THz -could be appropriate depending on the system. -

    -

    The random number seed is a positive integer used to initiate a -Marsaglia random number generator. Each processor uses the input seed -to generate its own unique seed and its own stream of random -numbers. Thus the dynamics of the system will not be identical on two -runs on different numbers of processors. -

    -

    The f_max parameter truncate the noise frequency domain so that -vibrational modes with frequencies higher than f_max will not be -modulated. If we denote Δt as the time interval for the -MD integration, f_max is always reset by the code to make -α = (int)(2f_maxΔt)-1 a -positive integer and print out relative information. An appropriate -value for the cutoff frequency f_max would be around 2~3 -fD, where fD is the Debye -frequency. -

    -

    The N_f parameter is the frequency grid size, the number of points -from 0 to f_max in the frequency domain that will be -sampled. 3×2 N_f per-atom random numbers are required -in the random force generation and there could be as many atoms as in -the whole simulation that can migrate into every individual -processor. A larger N_f provides a more accurate sampling of the -spectrum while consumes more memory. With fixed f_max and -γ, N_f should be big enough to converge the classical -temperature Tcl as a function of target quantum bath -temperature. Memory usage per processor could be from 10 to 100 -Mbytes. -

    -

    IMPORTANT NOTE: Unlike the fix nvt command which -performs Nose/Hoover thermostatting AND time integration, this fix -does NOT perform time integration. It only modifies forces to a -colored thermostat. Thus you must use a separate time integration fix, -like fix nve or fix nph to actually -update the velocities and positions of atoms (as shown in the -examples). Likewise, this fix should not normally be used with other -fixes or commands that also specify system temperatures , e.g. fix -nvt and fix temp/rescale. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimizie info: -

    -

    No information about this fix is written to binary restart -files. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix. However, in a statistical sense, a restarted -simulation should produce similar behaviors of the system. -

    -

    This fix is not invoked during energy minimization. -

    -
    - -

    Restrictions: -

    -

    This fix style is part of the USER-QTB package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -
    - -

    Related commands: -

    -

    fix nve, fix nph, fix -langevin, fix qbmsst -

    -
    - -

    Default: -

    -

    The keyword defaults are temp = 300, damp = 1, seed = 880302, -f_max=200.0 and N_f = 100. -

    -
    - - - -

    (Dammak) Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev -Lett, 103, 190601 (2009). -

    - - -

    (Barrat) Barrat and Rodney, J. Stat. Phys, 144, 679 (2011). -

    - diff --git a/doc/doc2/fix_reax_bonds.html b/doc/doc2/fix_reax_bonds.html deleted file mode 100644 index dd25932e9c..0000000000 --- a/doc/doc2/fix_reax_bonds.html +++ /dev/null @@ -1,73 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix reax/bonds command -

    -

    fix reax/c/bonds command -

    -

    Syntax: -

    -
    fix ID group-ID reax/bonds Nevery filename 
-
    -
    • ID, group-ID are documented in fix command -
    • reax/bonds = style name of this fix command -
    • Nevery = output interval in timesteps -
    • filename = name of output file -
    -

    Examples: -

    -
    fix 1 all reax/bonds 100 bonds.tatb
-fix 1 all reax/c/bonds 100 bonds.reaxc 
-
    -

    Description: -

    -

    Write out the bond information computed by the ReaxFF potential -specified by pair_style reax or pair_style -reax/c in the exact same format as the original -stand-alone ReaxFF code of Adri van Duin. The bond information is -written to filename on timesteps that are multiples of Nevery, -including timestep 0. For time-averaged chemical species analysis, -please see the fix species command. -

    -

    The format of the output file should be self-explantory. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    The fix reax/bonds command requires that the pair_style -reax be invoked. This fix is part of the REAX -package. It is only enabled if LAMMPS was built with that package, -which also requires the REAX library be built and linked with LAMMPS. -The fix reax/c/bonds command requires that the pair_style -reax/c be invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the Making LAMMPS section -for more info. -

    -

    Related commands: -

    -

    pair_style reax, pair_style -reax/c, fix reax/c/species -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_reaxc_species.html b/doc/doc2/fix_reaxc_species.html deleted file mode 100644 index 2fadd7e7f7..0000000000 --- a/doc/doc2/fix_reaxc_species.html +++ /dev/null @@ -1,166 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix reax/c/species command -

    -

    Syntax: -

    -
    fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • reax/c/species = style name of this command - -
    • Nevery = sample bond-order every this many timesteps - -
    • Nrepeat = # of bond-order samples used for calculating averages - -
    • Nfreq = calculate average bond-order every this many timesteps - -
    • filename = name of output file - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = cutoff or element or position - -
        cutoff value = I J Cutoff
-    I, J = atom types
-    Cutoff = Bond-order cutoff value for this pair of atom types
-  element value = Element1, Element2, ... 
-  position value = posfreq filepos
-    posfreq = write position files every this many timestep
-    filepos = name of position output file 
-
      - -
    -

    Examples: -

    -
    fix 1 all reax/c/species 10 10 100 species.out
-fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
-fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos 
-
    -

    Description: -

    -

    Write out the chemical species information computed by the ReaxFF -potential specified by pair_style reax/c. -Bond-order values (either averaged or instantaneous, depending on -value of Nrepeat) are used to determine chemical bonds. Every -Nfreq timesteps, chemical species information is written to -filename as a two line output. The first line is a header -containing labels. The second line consists of the following: -timestep, total number of molecules, total number of distinct species, -number of molecules of each species. In this context, "species" means -a unique molecule. The chemical formula of each species is given in -the first line. -

    -

    Optional keyword cutoff can be assigned to change the minimum -bond-order values used in identifying chemical bonds between pairs of -atoms. Bond-order cutoffs should be carefully chosen, as bond-order -cutoffs that are too small may include too many bonds (which will -result in an error), while cutoffs that are too large will result in -fragmented molecules. The default cutoff of 0.3 usually gives good -results. -

    -

    The optional keyword element can be used to specify the chemical -symbol printed for each LAMMPS atom type. The number of symbols must -match the number of LAMMPS atom types and each symbol must consist of -1 or 2 alphanumeric characters. Normally, these symbols should be -chosen to match the chemical identity of each LAMMPS atom type, as -specified using the reax/c pair_coeff command and -the ReaxFF force field file. -

    -

    The optional keyword position writes center-of-mass positions of -each identified molecules to file filepos every posfreq timesteps. -The first line contains information on timestep, total number of -molecules, total number of distinct species, and box dimensions. The -second line is a header containing labels. From the third line -downward, each molecule writes a line of output containing the -following information: molecule ID, number of atoms in this molecule, -chemical formula, total charge, and center-of-mass xyz positions of -this molecule. The xyz positions are in fractional coordinates -relative to the box dimensions. -

    -

    For the keyword position, the filepos is the name of the output -file. It can contain the wildcard character "*". If the "*" -character appears in filepos, then one file per snapshot is written -at posfreq and the "*" character is replaced with the timestep -value. For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc. -

    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the bond-order values are sampled to get the average bond -order. The species analysis is performed using the average bond-order -on timesteps that are a multiple of Nfreq. The average is over -Nrepeat bond-order samples, computed in the preceding portion of the -simulation every Nevery timesteps. Nfreq must be a multiple of -Nevery and Nevery must be non-zero even if Nrepeat is 1. -Also, the timesteps -contributing to the average bond-order cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order -values on timesteps 90,92,94,96,98,100 will be used to compute the -average bond-order for the species analysis output on timestep 100. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes both a global vector of length 2 and a per-atom -vector, either of which can be accessed by various output -commands. The values in the global -vector are "intensive". -

    -

    The 2 values in the global vector are as follows: -

    -
    • 1 = total number of molecules -
    • 2 = total number of distinct species -
    -

    The per-atom vector stores the molecule ID for each atom as identified -by the fix. If an atom is not in a molecule, its ID will be 0. -For atoms in the same molecule, the molecule ID for all of them -will be the same and will be equal to the smallest atom ID of -any atom in the molecule. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    The fix species currently only works with -pair_style reax/c and it requires that the pair_style -reax/c be invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the Making LAMMPS section -for more info. -

    -

    It should be possible to extend it to other reactive pair_styles (such as -rebo, airebo, -comb, and bop), but this has not yet been done. -

    -

    Related commands: -

    -

    pair_style reax/c, fix -reax/bonds -

    -

    Default: -

    -

    The default values for bond-order cutoffs are 0.3 for all I-J pairs. The -default element symbols are C, H, O, N. Position files are not written -by default. -

    - diff --git a/doc/doc2/fix_recenter.html b/doc/doc2/fix_recenter.html deleted file mode 100644 index 0213e10742..0000000000 --- a/doc/doc2/fix_recenter.html +++ /dev/null @@ -1,136 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix recenter command -

    -

    Syntax: -

    -
    fix ID group-ID recenter x y z keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • recenter = style name of this fix command - -
    • x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = shift or units - -
        shift value = group-ID
-    group-ID = group of atoms whose coords are shifted
-  units value = box or lattice or fraction 
-
      - -
    -

    Examples: -

    -
    fix 1 all recenter 0.0 0.5 0.0
-fix 1 all recenter INIT INIT NULL
-fix 1 all recenter INIT 0.0 0.0 units box 
-
    -

    Description: -

    -

    Constrain the center-of-mass position of a group of atoms by adjusting -the coordinates of the atoms every timestep. This is simply a small -shift that does not alter the dynamics of the system or change the -relative coordinates of any pair of atoms in the group. This can be -used to insure the entire collection of atoms (or a portion of them) -do not drift during the simulation due to random perturbations -(e.g. fix langevin thermostatting). -

    -

    Distance units for the x,y,z values are determined by the setting of -the units keyword, as discussed below. One or more x,y,z values can -also be specified as NULL, which means exclude that dimension from -this operation. Or it can be specified as INIT which means to -constrain the center-of-mass to its initial value at the beginning of -the run. -

    -

    The center-of-mass (COM) is computed for the group specified by the -fix. If the current COM is different than the specified x,y,z, then a -group of atoms has their coordinates shifted by the difference. By -default the shifted group is also the group specified by the fix. A -different group can be shifted by using the shift keyword. For -example, the COM could be computed on a protein to keep it in the -center of the simulation box. But the entire system (protein + water) -could be shifted. -

    -

    If the units keyword is set to box, then the distance units of -x,y,z are defined by the units command - e.g. Angstroms -for real units. A lattice value means the distance units are in -lattice spacings. The lattice command must have been -previously used to define the lattice spacing. A fraction value -means a fractional distance between the lo/hi box boundaries, e.g. 0.5 -= middle of the box. The default is to use lattice units. -

    -

    Note that the velocity command can be used to create -velocities with zero aggregate linear and/or angular momentum. -

    -

    IMPORTANT NOTE: This fix performs its operations at the same point in -the timestep as other time integration fixes, such as fix -nve, fix nvt, or fix npt. -Thus fix recenter should normally be the last such fix specified in -the input script, since the adjustments it makes to atom coordinates -should come after the changes made by time integration. LAMMPS will -warn you if your fixes are not ordered this way. -

    -

    IMPORTANT NOTE: If you use this fix on a small group of atoms (e.g. a -molecule in solvent) without using the shift keyword to adjust the -positions of all atoms in the system, then the results can be -unpredictable. For example, if the molecule is pushed in one -direction by the solvent, its velocity will increase. But its -coordinates will be recentered, meaning it is pushed back towards the -force. Thus over time, the velocity and temperature of the molecule -could become very large (though it won't appear to be moving due to -the recentering). If you are thermostatting the entire system, then -the solvent would be cooled to compensate. A better solution for this -simulation scenario is to use the fix spring command -to tether the molecule in place. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -distance the group is moved by fix recenter. -

    -

    This fix also computes global 3-vector which can be accessed by -various output commands. The 3 -quantities in the vector are xyz components of displacement applied to -the group of atoms by the fix. -

    -

    The scalar and vector values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix should not be used with an x,y,z setting that causes a large -shift in the system on the 1st timestep, due to the requested COM -being very different from the initial COM. This could cause atoms to -be lost, especially in parallel. Instead, use the -displace_atoms command, which can be used to -move atoms a large distance. -

    -

    Related commands: -

    -

    fix momentum, velocity -

    -

    Default: -

    -

    The option defaults are shift = fix group-ID, and units = lattice. -

    - diff --git a/doc/doc2/fix_restrain.html b/doc/doc2/fix_restrain.html deleted file mode 100644 index ae650575a3..0000000000 --- a/doc/doc2/fix_restrain.html +++ /dev/null @@ -1,193 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix restrain command -

    -

    Syntax: -

    -
    fix ID group-ID restrain keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • restrain = style name of this fix command - -
    • one or more keyword/arg pairs may be appended - -
    • keyword = bond or angle or dihedral - -
        bond args = atom1 atom2 Kstart Kstop r0
-    atom1,atom2 = IDs of 2 atoms in bond
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    r0 = equilibrium bond distance (distance units)
-  angle args = atom1 atom2 atom3 Kstart Kstop theta0
-    atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    theta0 = equilibrium angle theta (degrees)
-  dihedral args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
-    atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    phi0 = equilibrium dihedral angle phi (degrees) 
-
      - -
    -

    Examples: -

    -
    fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
-fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
-fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
-fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 
-
    -

    Description: -

    -

    Restrain the motion of the specified sets of atoms by making them part -of a bond or angle or dihedral interaction whose strength can vary -over time during a simulation. This is functionally equivalent to -creating a bond or angle or dihedral for the same atoms in a data -file, as specified by the read_data command, albeit -with a time-varying pre-factor coefficient. For the purpose of -forcefield parameter-fitting or mapping a molecular potential energy -surface, this fix reduces the hassle and risk associated with -modifying data files. In other words, use this fix to temporarily -force a molecule to adopt a particular conformation. To create a -permanent bond or angle or dihedral, you should modify the data file. -

    -

    The group-ID specified by this fix is ignored. -

    -

    The second example above applies a restraint to hold the dihedral -angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant -restraint coefficient. The fourth example applies similar restraints -to multiple dihedral angles using a restraint coefficient that -increases from 0.0 to 2000.0 over the course of the run. -

    -

    IMPORTANT NOTE: Adding a force to atoms implies a change in their -potential energy as they move due to the applied force field. For -dynamics via the run command, this energy can be added to -the system's potential energy for thermodynamic output (see below). -For energy minimization via the minimize command, this -energy must be added to the system's potential energy to formulate a -self-consistent minimization problem (see below). -

    -

    In order for a restraint to be effective, the restraint force must -typically be significantly larger than the forces associated with -conventional forcefield terms. If the restraint is applied during a -dynamics run (as opposed to during an energy minimization), a large -restraint coefficient can significantly reduce the stable timestep -size, especially if the atoms are initially far from the preferred -conformation. You may need to experiment to determine what value of K -works best for a given application. -

    -

    For the case of finding a minimum energy structure for a single -molecule with particular restratins (e.g. for fitting forcefield -parameters or constructing a potential energy surface), commands such -as the following may be useful: -

    -
    # minimize molecule energy with restraints
-velocity all create 600.0 8675309 mom yes rot yes dist gaussian
-fix NVE all nve
-fix TFIX all langevin 600.0 0.0 100 24601
-fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2}
-fix_modify REST energy yes
-run 10000
-fix TFIX all langevin 0.0 0.0 100 24601
-fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2}
-fix_modify REST energy yes
-run 10000
-# sanity check for convergence
-minimize 1e-6 1e-9 1000 100000
-# report unrestrained energies
-unfix REST
-run 0 
-
    -
    - -

    The bond keyword applies a bond restraint to the specified atoms -using the same functional form used by the bond_style -harmonic command. The potential associated with -the restraint is -

    -
    -
    -

    with the following coefficients: -

    -
    • K (energy/distance^2) -
    • r0 (distance) -
    -

    K and r0 are specified with the fix. Note that the usual 1/2 factor -is included in K. -

    -
    - -

    The angle keyword applies an angle restraint to the specified atoms -using the same functional form used by the angle_style -harmonic command. The potential associated with -the restraint is -

    -
    -
    -

    with the following coefficients: -

    -
    • K (energy/radian^2) -
    • theta0 (degrees) -
    -

    K and theta0 are specified with the fix. Note that the usual 1/2 -factor is included in K. -

    -
    - -

    The dihedral keyword applies a dihedral restraint to the specified -atoms using a simplified form of the function used by the -dihedral_style charmm command. The potential -associated with the restraint is -

    -
    -
    -

    with the following coefficients: -

    -
    • K (energy) -
    • n = 1 -
    • d (degrees) = phi0 + 180 -
    -

    K and phi0 are specified with the fix. Note that the value of n is -hard-wired to 1. Also note that the energy will be a minimum when the -current dihedral angle phi is equal to phi0. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the potential energy associated with this fix to the -system's potential energy as part of thermodynamic -output. -

    -

    IMPORTANT NOTE: If you want the fictitious potential energy associated -with the added forces to be included in the total potential energy of -the system (the quantity being minimized), you MUST enable the -fix_modify energy option for this fix. -

    -

    This fix computes a global scalar, which can be accessed by various -output commands. The scalar is the -potential energy for all the restraints as discussed above. The scalar -value calculated by this fix is "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_rigid.html b/doc/doc2/fix_rigid.html deleted file mode 100644 index 971bfd479e..0000000000 --- a/doc/doc2/fix_rigid.html +++ /dev/null @@ -1,814 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix rigid command -

    -

    fix rigid/nve command -

    -

    fix rigid/nvt command -

    -

    fix rigid/npt command -

    -

    fix rigid/nph command -

    -

    fix rigid/small command -

    -

    fix rigid/nve/small command -

    -

    fix rigid/nvt/small command -

    -

    fix rigid/npt/small command -

    -

    fix rigid/nph/small command -

    -

    Syntax: -

    -
    fix ID group-ID style bodystyle args keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • style = rigid or rigid/nve or rigid/nvt or rigid/npt or rigid/nph or rigid/small or rigid/nve/small or rigid/nvt/small or rigid/npt/small or rigid/nph/small - -
    • bodystyle = single or molecule or group - -
        single args = none
-  molecule args = none
-  group args = N groupID1 groupID2 ...
-    N = # of groups
-    groupID1, groupID2, ... = list of N group IDs 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = langevin or temp or iso or aniso or x or y or z or couple or tparam or pchain or dilate or force or torque or infile - -
        langevin values = Tstart Tstop Tperiod seed
-    Tstart,Tstop = desired temperature at start/stop of run (temperature units)
-    Tdamp = temperature damping parameter (time units)
-    seed = random number seed to use for white noise (positive integer)
-  temp values = Tstart Tstop Tdamp
-    Tstart,Tstop = desired temperature at start/stop of run (temperature units)
-    Tdamp = temperature damping parameter (time units)
-  iso or aniso values = Pstart Pstop Pdamp
-    Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
-    Pdamp = pressure damping parameter (time units)
-  x or y or z values = Pstart Pstop Pdamp
-    Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
-    Pdamp = stress damping parameter (time units)
-  couple = none or xyz or xy or yz or xz
-  tparam values = Tchain Titer Torder
-    Tchain = length of Nose/Hoover thermostat chain
-    Titer = number of thermostat iterations performed
-    Torder = 3 or 5 = Yoshida-Suzuki integration parameters
-  pchain values = Pchain
-    Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
-  dilate value = dilate-group-ID
-    dilate-group-ID = only dilate atoms in this group due to barostat volume changes
-  force values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass force is active
-  torque values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass torque is active
-  infile filename
-    filename = file with per-body values of mass, center-of-mass, moments of inertia 
-  mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command 
-
      - -
    -

    Examples: -

    -
    fix 1 clump rigid single
-fix 1 clump rigid/small molecule
-fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
-fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
-fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
-fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
-fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off 
-fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
-fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
-fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
-fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 
-
    -

    Description: -

    -

    Treat one or more sets of atoms as independent rigid bodies. This -means that each timestep the total force and torque on each rigid body -is computed as the sum of the forces and torques on its constituent -particles. The coordinates, velocities, and orientations of the atoms -in each body are then updated so that the body moves and rotates as a -single entity. -

    -

    Examples of large rigid bodies are a colloidal particle, or portions -of a biomolecule such as a protein. -

    -

    Example of small rigid bodies are patchy nanoparticles, such as those -modeled in this paper by Sharon Glotzer's group, clumps of -granular particles, lipid molecules consiting of one or more point -dipoles connected to other spheroids or ellipsoids, irregular -particles built from line segments (2d) or triangles (3d), and -coarse-grain models of nano or colloidal particles consisting of a -small number of constituent particles. Note that the fix -shake command can also be used to rigidify small -molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats -the constituent atoms as point masses. -

    -

    These fixes also update the positions and velocities of the atoms in -each rigid body via time integration, in the NVE, NVT, NPT, or NPH -ensemble, as described below. -

    -

    There are two main variants of this fix, fix rigid and fix -rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two -variants, as their style names indicate. -

    -

    IMPORTANT NOTE: Not all of the bodystyle options and keyword/value -options are available for both the rigid and rigid/small variants. -See details below. -

    -

    The rigid variant is typically the best choice for a system with a -small number of large rigid bodies, each of which can extend across -the domain of many processors. It operates by creating a single -global list of rigid bodies, which all processors contribute to. -MPI_Allreduce operations are performed each timestep to sum the -contributions from each processor to the force and torque on all the -bodies. This operation will not scale well in parallel if large -numbers of rigid bodies are simulated. -

    -

    The rigid/small variant is typically best for a system with a large -number of small rigid bodies. Each body is assigned to the atom -closest to the geometrical center of the body. The fix operates using -local lists of rigid bodies owned by each processor and information is -exchanged and summed via local communication between neighboring -processors when ghost atom info is accumlated. -

    -

    IMPORTANT NOTE: To use rigid/small the ghost atom cutoff must be -large enough to span the distance between the atom that owns the body -and every other atom in the body. This distance value is printed out -when the rigid bodies are defined. If the -pair_style cutoff plus neighbor skin does not span -this distance, then you should use the comm_modify -cutoff command with a setting epsilon larger than -the distance. -

    -

    Which of the two variants is faster for a particular problem is hard -to predict. The best way to decide is to perform a short test run. -Both variants should give identical numerical answers for short runs. -Long runs should give statistically similar results, but round-off -differences may accumulate to produce divergent trajectories. -

    -

    IMPORTANT NOTE: You should not update the atoms in rigid bodies via -other time-integration fixes (e.g. fix nve, fix -nvt, fix npt), or you will be integrating -their motion more than once each timestep. When performing a hybrid -simulation with some atoms in rigid bodies, and some not, a separate -time integration fix like fix nve or fix -nvt should be used for the non-rigid particles. -

    -

    IMPORTANT NOTE: These fixes are overkill if you simply want to hold a -collection of atoms stationary or have them move with a constant -velocity. A simpler way to hold atoms stationary is to not include -those atoms in your time integration fix. E.g. use "fix 1 mobile nve" -instead of "fix 1 all nve", where "mobile" is the group of atoms that -you want to move. You can move atoms with a constant velocity by -assigning them an initial velocity (via the velocity -command), setting the force on them to 0.0 (via the fix -setforce command), and integrating them as usual -(e.g. via the fix nve command). -

    -

    IMPORTANT NOTE: The aggregate properties of each rigid body are -calculated one time at the start of the first simulation run after -this fix is specified. The properties include the position and -velocity of the center-of-mass of the body, its moments of inertia, -and its angular momentum. This is done using the properties of the -constituent atoms of the body at that point in time (or see the -infile keyword option). Thereafter, changing properties of -individual atoms in the body will have no effect on a rigid body's -dynamics, unless they effect the pair_style -interactions that individual particles are part of. For example, you -might think you could displace the atoms in a body or add a large -velocity to each atom in a body to make it move in a desired direction -before a 2nd run is performed, using the set or -displace_atoms or velocity -command. But these commands will not affect the internal attributes -of the body, and the position and velocity or individual atoms in the -body will be reset when time integration starts. -

    -
    - -

    Each rigid body must have two or more atoms. An atom can belong to at -most one rigid body. Which atoms are in which bodies can be defined -via several options. -

    -

    IMPORTANT NOTE: With fix rigid/small, which requires bodystyle -molecule, you can define a system that has no rigid bodies -initially. This is useful when you are using the mol keyword in -conjunction with another fix that is adding rigid bodies on-the-fly, -such as fix deposit or fix pour. -

    -

    For bodystyle single the entire fix group of atoms is treated as one -rigid body. This option is only allowed for fix rigid and its -sub-styles. -

    -

    For bodystyle molecule, each set of atoms in the fix group with a -different molecule ID is treated as a rigid body. This option is -allowed for fix rigid and fix rigid/small, and their sub-styles. Note -that atoms with a molecule ID = 0 will be treated as a single rigid -body. For a system with atomic solvent (typically this is atoms with -molecule ID = 0) surrounding rigid bodies, this may not be what you -want. Thus you should be careful to use a fix group that only -includes atoms you want to be part of rigid bodies. -

    -

    For bodystyle group, each of the listed groups is treated as a -separate rigid body. Only atoms that are also in the fix group are -included in each rigid body. This option is only allowed for fix -rigid and its sub-styles. -

    -

    IMPORTANT NOTE: To compute the initial center-of-mass position and -other properties of each rigid body, the image flags for each atom in -the body are used to "unwrap" the atom coordinates. Thus you must -insure that these image flags are consistent so that the unwrapping -creates a valid rigid body (one where the atoms are close together), -particularly if the atoms in a single rigid body straddle a periodic -boundary. This means the input data file or restart file must define -the image flags for each atom consistently or that you have used the -set command to specify them correctly. If a dimension is -non-periodic then the image flag of each atom must be 0 in that -dimension, else an error is generated. -

    -

    The force and torque keywords discussed next are only allowed for -fix rigid and its sub-styles. -

    -

    By default, each rigid body is acted on by other atoms which induce an -external force and torque on its center of mass, causing it to -translate and rotate. Components of the external center-of-mass force -and torque can be turned off by the force and torque keywords. -This may be useful if you wish a body to rotate but not translate, or -vice versa, or if you wish it to rotate or translate continuously -unaffected by interactions with other particles. Note that if you -expect a rigid body not to move or rotate by using these keywords, you -must insure its initial center-of-mass translational or angular -velocity is 0.0. Otherwise the initial translational or angular -momentum the body has will persist. -

    -

    An xflag, yflag, or zflag set to off means turn off the component of -force of torque in that dimension. A setting of on means turn on -the component, which is the default. Which rigid body(s) the settings -apply to is determined by the first argument of the force and -torque keywords. It can be an integer M from 1 to Nbody, where -Nbody is the number of rigid bodies defined. A wild-card asterisk can -be used in place of, or in conjunction with, the M argument to set the -flags for multiple rigid bodies. This takes the form "*" or "*n" or -"n*" or "m*n". If N = the number of rigid bodies, then an asterisk -with no numeric values means all bodies from 1 to N. A leading -asterisk means all bodies from 1 to n (inclusive). A trailing -asterisk means all bodies from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). Note that you can use the -force or torque keywords as many times as you like. If a -particular rigid body has its component flags set multiple times, the -settings from the final keyword are used. -

    -

    IMPORTANT NOTE: For computational efficiency, you may wish to turn off -pairwise and bond interactions within each rigid body, as they no -longer contribute to the motion. The neigh_modify -exclude and delete_bonds -commands are used to do this. If the rigid bodies have strongly -overalapping atoms, you may need to turn off these interactions to -avoid numerical problems due to large equal/opposite intra-body forces -swamping the contribution of small inter-body forces. -

    -

    For computational efficiency, you should typically define one fix -rigid or fix rigid/small command which includes all the desired rigid -bodies. LAMMPS will allow multiple rigid fixes to be defined, but it -is more expensive. -

    -
    - -

    The constituent particles within a rigid body can be point particles -(the default in LAMMPS) or finite-size particles, such as spheres or -ellipsoids or line segments or triangles. See the atom_style sphere -and ellipsoid and line and tri commands for more -details on these kinds of particles. Finite-size particles contribute -differently to the moment of inertia of a rigid body than do point -particles. Finite-size particles can also experience torque (e.g. due -to frictional granular interactions) and have an -orientation. These contributions are accounted for by these fixes. -

    -

    Forces between particles within a body do not contribute to the -external force or torque on the body. Thus for computational -efficiency, you may wish to turn off pairwise and bond interactions -between particles within each rigid body. The neigh_modify -exclude and delete_bonds -commands are used to do this. For finite-size particles this also -means the particles can be highly overlapped when creating the rigid -body. -

    -
    - -

    The rigid and rigid/small and rigid/nve styles perform constant -NVE time integration. The only difference is that the rigid and -rigid/small styles use an integration technique based on Richardson -iterations. The rigid/nve style uses the methods described in the -paper by Miller, which are thought to provide better energy -conservation than an iterative approach. -

    -

    The rigid/nvt and rigid/nvt/small styles performs constant NVT -integration using a Nose/Hoover thermostat with chains as described -originally in (Hoover) and (Martyna), which -thermostats both the translational and rotational degrees of freedom -of the rigid bodies. The rigid-body algorithm used by rigid/nvt -is described in the paper by Kamberaj. -

    -

    The rigid/npt and rigid/nph (and their /small counterparts) styles -perform constant NPT or NPH integration using a Nose/Hoover barostat -with chains. For the NPT case, the same Nose/Hoover thermostat is also -used as with rigid/nvt. -

    -

    The barostat parameters are specified using one or more of the iso, -aniso, x, y, z and couple keywords. These keywords give you -the ability to specify 3 diagonal components of the external stress -tensor, and to couple these components together so that the dimensions -they represent are varied together during a constant-pressure -simulation. The effects of these keywords are similar to those -defined in fix npt/nph -

    -

    NOTE: Currently the rigid/npt and rigid/nph (and their /small -counterparts) styles do not support triclinic (non-orthongonal) boxes. -

    -

    The target pressures for each of the 6 components of the stress tensor -can be specified independently via the x, y, z keywords, which -correspond to the 3 simulation box dimensions. For each component, -the external pressure or tensor component at each timestep is a ramped -value during the run from Pstart to Pstop. If a target pressure is -specified for a component, then the corresponding box dimension will -change during a simulation. For example, if the y keyword is used, -the y-box length will change. A box dimension will not change if that -component is not specified, although you have the option to change -that dimension via the fix deform command. -

    -

    For all barostat keywords, the Pdamp parameter operates like the -Tdamp parameter, determining the time scale on which pressure is -relaxed. For example, a value of 10.0 means to relax the pressure in -a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see -the units command). -

    -

    Regardless of what atoms are in the fix group (the only atoms which -are time integrated), a global pressure or stress tensor is computed -for all atoms. Similarly, when the size of the simulation box is -changed, all atoms are re-scaled to new positions, unless the keyword -dilate is specified with a dilate-group-ID for a group that -represents a subset of the atoms. This can be useful, for example, to -leave the coordinates of atoms in a solid substrate unchanged and -controlling the pressure of a surrounding fluid. Another example is a -system consisting of rigid bodies and point particles where the -barostat is only coupled with the rigid bodies. This option should be -used with care, since it can be unphysical to dilate some atoms and -not others, because it can introduce large, instantaneous -displacements between a pair of atoms (one dilated, one not) that are -far from the dilation origin. -

    -

    The couple keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, xz -means the Pxx and Pzz components of the stress tensor are coupled. -Xyz means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -Pstart, Pstop, Pdamp parameters for any coupled dimensions must -be identical. Couple xyz can be used for a 2d simulation; the z -dimension is simply ignored. -

    -

    The iso and aniso keywords are simply shortcuts that are -equivalent to specifying several other keywords together. -

    -

    The keyword iso means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Pstart Pstop Pdamp" is the same as -specifying these 4 keywords: -

    -
    x Pstart Pstop Pdamp
-y Pstart Pstop Pdamp
-z Pstart Pstop Pdamp
-couple xyz 
-
    -

    The keyword aniso means x, y, and z dimensions are controlled -independently using the Pxx, Pyy, and Pzz components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying -these 4 keywords: -

    -
    x Pstart Pstop Pdamp
-y Pstart Pstop Pdamp
-z Pstart Pstop Pdamp
-couple none 
-
    -
    - -

    The keyword/value option pairs are used in the following ways. -

    -

    The langevin and temp and tparam keywords perform thermostatting -of the rigid bodies, altering both their translational and rotational -degrees of freedom. What is meant by "temperature" of a collection of -rigid bodies and how it can be monitored via the fix output is -discussed below. -

    -

    The langevin keyword applies a Langevin thermostat to the constant -NVE time integration performed by either the rigid or rigid/small -or rigid/nve styles. It cannot be used with the rigid/nvt style. -The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The Tdamp parameter is specified in -time units and determines how rapidly the temperature is relaxed. For -example, a value of 100.0 means to relax the temperature in a timespan -of (roughly) 100 time units (tau or fmsec or psec - see the -units command). The random # seed must be a positive -integer. -

    -

    The way that Langevin thermostatting operates is explained on the fix -langevin doc page. If you wish to simply viscously -damp the rotational motion without thermostatting, you can set -Tstart and Tstop to 0.0, which means only the viscous drag term in -the Langevin thermostat will be applied. See the discussion on the -fix viscous doc page for details. -

    -

    IMPORTANT NOTE: When the langevin keyword is used with fix rigid -versus fix rigid/small, different dynamics will result for parallel -runs. This is because of the way random numbers are used in the two -cases. The dynamics for the two cases should be statistically -similar, but will not be identical, even for a single timestep. -

    -

    The temp and tparam keywords apply a Nose/Hoover thermostat to the -NVT time integration performed by the rigid/nvt style. They cannot -be used with the rigid or rigid/small or rigid/nve styles. The -desired temperature at each timestep is a ramped value during the run -from Tstart to Tstop. The Tdamp parameter is specified in time -units and determines how rapidly the temperature is relaxed. For -example, a value of 100.0 means to relax the temperature in a timespan -of (roughly) 100 time units (tau or fmsec or psec - see the -units command). -

    -

    Nose/Hoover chains are used in conjunction with this thermostat. The -tparam keyword can optionally be used to change the chain settings -used. Tchain is the number of thermostats in the Nose Hoover chain. -This value, along with Tdamp can be varied to dampen undesirable -oscillations in temperature that can occur in a simulation. As a rule -of thumb, increasing the chain length should lead to smaller -oscillations. The keyword pchain specifies the number of -thermostats in the chain thermostatting the barostat degrees of -freedom. -

    -

    IMPORTANT NOTE: There are alternate ways to thermostat a system of -rigid bodies. You can use fix langevin to treat -the individual particles in the rigid bodies as effectively immersed -in an implicit solvent, e.g. a Brownian dynamics model. For hybrid -systems with both rigid bodies and solvent particles, you can -thermostat only the solvent particles that surround one or more rigid -bodies by appropriate choice of groups in the compute and fix commands -for temperature and thermostatting. The solvent interactions with the -rigid bodies should then effectively thermostat the rigid body -temperature as well without use of the Langevin or Nose/Hoover options -associated with the fix rigid commands. -

    -
    - -

    The mol keyword can only be used with fix rigid/small. It must be -used when other commands, such as fix deposit or -fix pour, add rigid bodies on-the-fly during a -simulation. You specify a template-ID previously defined using the -molecule command, which reads a file that defines the -molecule. You must use the same template-ID that the other fix -which is adding rigid bodies uses. The coordinates, atom types, atom -diameters, center-of-mass, and moments of inertia can be specified in -the molecule file. See the molecule command for -details. The only settings required to be in this file are the -coordinates and types of atoms in the molecule, in which case the -molecule command calculates the other quantities itself. -

    -

    Note that these other fixes create new rigid bodies, in addition to -those defined initially by this fix via the bodystyle setting. -

    -

    Also note that when using the mol keyword, extra restart information -about all rigid bodies is written out whenever a restart file is -written out. See the IMPORTANT NOTE in the next section for details. -

    -
    - -

    The infile keyword allows a file of rigid body attributes to be read -in from a file, rather then having LAMMPS compute them. There are 5 -such attributes: the total mass of the rigid body, its center-of-mass -position, its 6 moments of inertia, its center-of-mass velocity, and -the 3 image flags of the center-of-mass position. For rigid bodies -consisting of point particles or non-overlapping finite-size -particles, LAMMPS can compute these values accurately. However, for -rigid bodies consisting of finite-size particles which overlap each -other, LAMMPS will ignore the overlaps when computing these 4 -attributes. The amount of error this induces depends on the amount of -overlap. To avoid this issue, the values can be pre-computed -(e.g. using Monte Carlo integration). -

    -

    The format of the file is as follows. Note that the file does not -have to list attributes for every rigid body integrated by fix rigid. -Only bodies which the file specifies will have their computed -attributes overridden. The file can contain initial blank lines or -comment lines starting with "#" which are ignored. The first -non-blank, non-comment line should list N = the number of lines to -follow. The N successive lines contain the following information: -

    -
    ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
-ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
-...
-IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm 
-
    -

    The rigid body IDs are all positive integers. For the single -bodystyle, only an ID of 1 can be used. For the group bodystyle, -IDs from 1 to Ng can be used where Ng is the number of specified -groups. For the molecule bodystyle, use the molecule ID for the -atoms in a specific rigid body as the rigid body ID. -

    -

    The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are -self-explanatory. The center-of-mass should be consistent with what -is calculated for the position of the rigid body with all its atoms -unwrapped by their respective image flags. If this produces a -center-of-mass that is outside the simulation box, LAMMPS wraps it -back into the box. -

    -

    The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the -values consistent with the current orientation of the rigid body -around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the prinicpal axes of the -rigid body itself. LAMMPS performs the latter calculation internally. -

    -

    The (vxcm,vycm,vzcm) values are the velocity of the center of mass. -The (lx,ly,lz) values are the angular momentum of the body. The -(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you -wish the body to have no initial motion. -

    -

    The (ixcm,iycm,izcm) values are the image flags of the center of mass -of the body. For periodic dimensions, they specify which image of the -simulation box the body is considered to be in. An image of 0 means -it is inside the box as defined. A value of 2 means add 2 box lengths -to get the true value. A value of -1 means subtract 1 box length to -get the true value. LAMMPS updates these flags as the rigid bodies -cross periodic boundaries during the simulation. -

    -

    IMPORTANT NOTE: If you use the infile or mol keywords and write -restart files during a simulation, then each time a restart file is -written, the fix also write an auxiliary restart file with the name -rfile.rigid, where "rfile" is the name of the restart file, -e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary -file is in the same format described above. Thus it can be used in a -new input script that restarts the run and re-specifies a rigid fix -using an infile keyword and the appropriate filename. Note that the -auxiliary file will contain one line for every rigid body, even if the -original file only listed a subset of the rigid bodies. -

    -
    - -

    If you use a temperature compute with a group that -includes particles in rigid bodies, the degrees-of-freedom removed by -each rigid body are accounted for in the temperature (and pressure) -computation, but only if the temperature group includes all the -particles in a particular rigid body. -

    -

    A 3d rigid body has 6 degrees of freedom (3 translational, 3 -rotational), except for a collection of point particles lying on a -straight line, which has only 5, e.g a dimer. A 2d rigid body has 3 -degrees of freedom (2 translational, 1 rotational). -

    -

    IMPORTANT NOTE: You may wish to explicitly subtract additional -degrees-of-freedom if you use the force and torque keywords to -eliminate certain motions of one or more rigid bodies. LAMMPS does -not do this automatically. -

    -

    The rigid body contribution to the pressure of the system (virial) is -also accounted for by this fix. -

    -
    - -

    If your simlulation is a hybrid model with a mixture of rigid bodies -and non-rigid particles (e.g. solvent) there are several ways these -rigid fixes can be used in tandem with fix nve, fix -nvt, fix npt, and fix nph. -

    -

    If you wish to perform NVE dynamics (no thermostatting or -barostatting), use fix rigid or fix rigid/nve to integrate the rigid -bodies, and fix nve to integrate the non-rigid -particles. -

    -

    If you wish to perform NVT dynamics (thermostatting, but no -barostatting), you can use fix rigid/nvt for the rigid bodies, and any -thermostatting fix for the non-rigid particles (fix nvt, -fix langevin, fix -temp/berendsen). You can also use fix rigid -or fix rigid/nve for the rigid bodies and thermostat them using fix -langevin on the group that contains all the -particles in the rigid bodies. The net force added by fix -langevin to each rigid body effectively thermostats -its translational center-of-mass motion. Not sure how well it does at -thermostatting its rotational motion. -

    -

    If you with to perform NPT or NPH dynamics (barostatting), you cannot -use both fix npt and fix rigid/npt (or the nph -variants). This is because there can only be one fix which monitors -the global pressure and changes the simulation box dimensions. So you -have 3 choices: -

    -
    • Use fix rigid/npt for the rigid bodies. Use the dilate all option -so that it will dilate the positions of the non-rigid particles as -well. Use fix nvt (or any other thermostat) for the -non-rigid particles. - -
    • Use fix npt for the group of non-rigid particles. Use -the dilate all option so that it will dilate the center-of-mass -positions of the rigid bodies as well. Use fix rigid/nvt for the -rigid bodies. - -
    • Use fix press/berendsen to compute the -pressure and change the box dimensions. Use fix rigid/nvt for the -rigid bodies. Use fix nvt (or any other thermostat) for -the non-rigid particles. -
    -

    In all case, the rigid bodies and non-rigid particles both contribute -to the global pressure and the box is scaled the same by any of the -barostatting fixes. -

    -

    You could even use the 2nd and 3rd options for a non-hybrid simulation -consisting of only rigid bodies, assuming you give fix -npt an empty group, though it's an odd thing to do. The -barostatting fixes (fix npt and fix -press/berensen) will monitor the pressure -and change the box dimensions, but not time integrate any particles. -The integration of the rigid bodies will be performed by fix -rigid/nvt. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about the rigid and rigid/small and rigid/nve -fixes are written to binary restart files. The -exception is if the infile or mol keyword is used, in which case -an auxiliary file is written out with rigid body information each time -a restart file is written, as explained above for the infile -keyword. For style rigid/nvt the state of the Nose/Hoover -thermostat is written to binary restart files. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    The fix_modify energy option is supported by the -rigid/nvt fix to add the energy change induced by the thermostatting -to the system's potential energy as part of thermodynamic -output. -

    -

    The fix_modify temp and press options are -supported by the rigid/npt and rigid/nph fixes to change the computes used -to calculate the instantaneous pressure tensor. Note that the rigid/nvt fix -does not use any external compute to compute instantaneous temperature. -

    -

    The rigid and rigid/small and rigid/nve fixes compute a global -scalar which can be accessed by various output -commands. The scalar value calculated by -these fixes is "intensive". The scalar is the current temperature of -the collection of rigid bodies. This is averaged over all rigid -bodies and their translational and rotational degrees of freedom. The -translational energy of a rigid body is 1/2 m v^2, where m = total -mass of the body and v = the velocity of its center of mass. The -rotational energy of a rigid body is 1/2 I w^2, where I = the moment -of inertia tensor of the body and w = its angular velocity. Degrees -of freedom constrained by the force and torque keywords are -removed from this calculation, but only for the rigid and -rigid/nve fixes. -

    -

    The rigid/nvt, rigid/npt, and rigid/nph fixes compute a global -scalar which can be accessed by various output -commands. The scalar value calculated by -these fixes is "extensive". The scalar is the cumulative energy -change due to the thermostatting and barostatting the fix performs. -

    -

    All of the rigid fixes except rigid/small compute a global array -of values which can be accessed by various output -commands. The number of rows in the -array is equal to the number of rigid bodies. The number of columns -is 15. Thus for each rigid body, 15 values are stored: the xyz coords -of the center of mass (COM), the xyz components of the COM velocity, -the xyz components of the force acting on the COM, the xyz components -of the torque acting on the COM, and the xyz image flags of the COM. -

    -

    The center of mass (COM) for each body is similar to unwrapped -coordinates written to a dump file. It will always be inside (or -slightly outside) the simulation box. The image flags have the same -meaning as image flags for atom positions (see the "dump" command). -This means you can calculate the unwrapped COM by applying the image -flags to the COM, the same as when unwrapped coordinates are written -to a dump file. -

    -

    The force and torque values in the array are not affected by the -force and torque keywords in the fix rigid command; they reflect -values before any changes are made by those keywords. -

    -

    The ordering of the rigid bodies (by row in the array) is as follows. -For the single keyword there is just one rigid body. For the -molecule keyword, the bodies are ordered by ascending molecule ID. -For the group keyword, the list of group IDs determines the ordering -of bodies. -

    -

    The array values calculated by these fixes are "intensive", meaning -they are independent of the number of atoms in the simulation. -

    -

    No parameter of these fixes can be used with the start/stop keywords -of the run command. These fixes are not invoked during -energy minimization. -

    -
    - -

    Restrictions: -

    -

    These fixes are all part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Assigning a temperature via the velocity create -command to a system with rigid bodies may not have -the desired outcome for two reasons. First, the velocity command can -be invoked before the rigid-body fix is invoked or initialized and the -number of adjusted degrees of freedom (DOFs) is known. Thus it is not -possible to compute the target temperature correctly. Second, the -assigned velocities may be partially canceled when constraints are -first enforced, leading to a different temperature than desired. A -workaround for this is to perform a run 0 command, which -insures all DOFs are accounted for properly, and then rescale the -temperature to the desired value before performing a simulation. For -example: -

    -
    velocity all create 300.0 12345
-run 0                             # temperature may not be 300K
-velocity all scale 300.0          # now it should be 
-
    -

    Related commands: -

    -

    delete_bonds, neigh_modify -exclude, fix shake -

    -

    Default: -

    -

    The option defaults are force * on on on and torque * on on on, -meaning all rigid bodies are acted on by center-of-mass force and -torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3. -

    -
    - - - -

    (Hoover) Hoover, Phys Rev A, 31, 1695 (1985). -

    - - -

    (Kamberaj) Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005). -

    - - -

    (Martyna) Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); -Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117. -

    - - -

    (Miller) Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, -J Chem Phys, 116, 8649 (2002). -

    - - -

    (Zhang) Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). -

    - diff --git a/doc/doc2/fix_saed_vtk.html b/doc/doc2/fix_saed_vtk.html deleted file mode 100644 index c9367708a8..0000000000 --- a/doc/doc2/fix_saed_vtk.html +++ /dev/null @@ -1,200 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix saed/vtk command -

    -

    Syntax: -

    -
    fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • saed/vtk = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • Nrepeat = # of times to use input values for calculating averages - -
    • Nfreq = calculate averages every this many timesteps - -
    • c_ID = saed compute ID - -
      keyword = file or ave or start or file or overwrite:l
-  ave args = one or running or window M
-    one = output a new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  start args = Nstart
-    Nstart = start averaging on this timestep
-  file arg = filename
-    filename = name of file to output time averages to 
-  overwrite arg = none = overwrite output file with only latest output 
-
      - -
    -

    Examples: -

    -
    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
-compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo 
-
    -
    fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed 
-
    -

    Description: -

    -

    Time average computed intensities from compute_saed and -write output to a file in the 3rd generation vtk image data format for -visualization directly in parallelized visualization software packages -like ParaView and VisIt. Note that if no time averaging is done, this -command can be used as a convenient way to simply output diffraction -intensities at a single snapshot. -

    -

    To produce output in the image data vtk format ghost data is added -outside the Kmax range assigned in the compute saed. The ghost data is -assigned a value of -1 and can be removed setting a minimum isovolume -of 0 within the vizualiziton software. SAED images can be created by -visualizing a spherical slice of the data that is centered at -R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda. -

    -

    The group specified within this command is ignored. However, note that -specified values may represent calculations performed by saed computes -which store their own "group" definitions. -

    -

    Fix saed/vtk is designed to work only with compute_saed -values, e.g. -

    -
    compute 3 top saed 0.0251 Al O 
-fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed 
-
    -
    - -

    The Nevery, Nrepeat, and Nfreq arguments specify on what -timesteps the input values will be used in order to contribute to the -average. The final averaged quantities are generated on timesteps -that are a multiple of Nfreq. The average is over Nrepeat -quantities, computed in the preceding portion of the simulation every -Nevery timesteps. Nfreq must be a multiple of Nevery and -Nevery must be non-zero even if Nrepeat is 1. -Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. -

    -

    For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. -

    -
    - -

    The output for fix ave/time/saed is a file writen with the 3rd generation -vtk image data formatting. The filename assigned by the file keyword is -appended with _N.vtk where N is an index (0,1,2...) to account for multiple -diffraction intensity outputs. -

    -

    By default the header contains the following information (with example data): -

    -
    # vtk DataFile Version 3.0 c_SAED
-Image data set
-ASCII
-DATASET STRUCTURED_POINTS
-DIMENSIONS 337 219 209
-ASPECT_RATIO 0.00507953 0.00785161 0.00821458
-ORIGIN -0.853361 -0.855826 -0.854316 
-POINT_DATA 15424827
-SCALARS intensity float
-LOOKUP_TABLE default
-...data  
-
    -

    In this example, kspace is sampled across a 337 x 219 x 209 point mesh -where the mesh spacing is approximately 0.005, 0.007, and 0.008 -inv(length) units in the k1, k2, and k3 directions, respectively. -The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that -the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are -sampled in total. -

    -
    - -

    Additional optional keywords also affect the operation of this fix. -

    -

    The ave keyword determines how the values produced every Nfreq -steps are averaged with values produced on previous steps that were -multiples of Nfreq, before they are accessed by another output -command or written to a file. -

    -

    If the ave setting is one, then the values produced on timesteps -that are multiples of Nfreq are independent of each other; they are -output as-is without further averaging. -

    -

    If the ave setting is running, then the values produced on -timesteps that are multiples of Nfreq are summed and averaged in a -cumulative sense before being output. Each output value is thus the -average of the value produced on that timestep with all preceding -values. This running average begins when the fix is defined; it can -only be restarted by deleting the fix via the unfix -command, or by re-defining the fix by re-specifying it. -

    -

    If the ave setting is window, then the values produced on -timesteps that are multiples of Nfreq are summed and averaged within -a moving "window" of time, so that the last M values are used to -produce the output. E.g. if M = 3 and Nfreq = 1000, then the output -on step 10000 will be the average of the individual values on steps -8000,9000,10000. Outputs on early steps will average over less than M -values if they are not available. -

    -

    The start keyword specifies what timestep averaging will begin on. -The default is step 0. Often input values can be 0.0 at time 0, so -setting start to a larger value can avoid including a 0.0 in a -running or windowed average. -

    -

    The file keyword allows a filename to be specified. Every Nfreq -steps, the vector of saed intensity data is written to a new file using -the 3rd generation vtk format. The base of each file is assigned by -the file keyword and this string is appended with _N.vtk where N is -an index (0,1,2...) to account for situations with multiple diffraction -intensity outputs. -

    -

    The overwrite keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the ave running setting. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    The attributes for fix_saed_vtk must match the values assigned in the -associated compute_saed command. -

    -

    Related commands: -

    -

    compute_saed -

    -

    Default: -

    -

    The option defaults are ave = one, start = 0, no file output. -

    -
    - - - -

    (Coleman) Coleman, Spearot, Capolungo, MSMSE, 21, 055020 -(2013). -

    - diff --git a/doc/doc2/fix_setforce.html b/doc/doc2/fix_setforce.html deleted file mode 100644 index da6ffb5d3f..0000000000 --- a/doc/doc2/fix_setforce.html +++ /dev/null @@ -1,129 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix setforce command -

    -

    fix setforce/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID setforce fx fy fz keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • setforce = style name of this fix command - -
    • fx,fy,fz = force component values - -
    • any of fx,fy,fz can be a variable (see below) - -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = region - -
        region value = region-ID
-    region-ID = ID of region atoms must be in to have added force 
-
      - -
    -

    Examples: -

    -
    fix freeze indenter setforce 0.0 0.0 0.0
-fix 2 edge setforce NULL 0.0 0.0
-fix 2 edge setforce NULL 0.0 v_oscillate 
-
    -

    Description: -

    -

    Set each component of force on each atom in the group to the specified -values fx,fy,fz. This erases all previously computed forces on the -atom, though additional fixes could add new forces. This command can -be used to freeze certain atoms in the simulation by zeroing their -force, either for running dynamics or performing an energy -minimization. For dynamics, this assumes their initial velocity is -also zero. -

    -

    Any of the fx,fy,fz values can be specified as NULL which means do not -alter the force component in that dimension. -

    -

    Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style variable, namely fx, -fy, fz. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -force component. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent force field. -

    -

    Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent force -field with optional time-dependence as well. -

    -

    If the region keyword is used, the atom must also be in the -specified geometric region in order to have force added -to it. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global 3-vector of forces, which can be accessed -by various output commands. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command, but you cannot set -forces to any value besides zero when performing a minimization. Use -the fix addforce command if you want to apply a -non-zero force to atoms during a minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix addforce, fix aveforce -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_shake.html b/doc/doc2/fix_shake.html deleted file mode 100644 index 9aedcf50ad..0000000000 --- a/doc/doc2/fix_shake.html +++ /dev/null @@ -1,247 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix shake command -

    -

    fix shake/cuda command -

    -

    fix rattle command -

    -

    Syntax: -

    -
    fix ID group-ID style tol iter N constraint values ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • style = shake or rattle = style name of this fix command - -
    • tol = accuracy tolerance of SHAKE solution - -
    • iter = max # of iterations in each SHAKE solution - -
    • N = print SHAKE statistics every this many timesteps (0 = never) - -
    • one or more constraint/value pairs are appended - -
    • constraint = b or a or t or m - -
        b values = one or more bond types
-  a values = one or more angle types
-  t values = one or more atom types
-  m value = one or more mass values 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = mol - -
        mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command 
-
      - -
    -

    Examples: -

    -
    fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
-fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
-fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
-fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31
-fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol 
-
    -

    Description: -

    -

    Apply bond and angle constraints to specified bonds and angles in the -simulation by either the SHAKE or RATTLE algorithms. This typically -enables a longer timestep. -

    -

    SHAKE vs RATTLE: -

    -

    The SHAKE algorithm was invented for schemes such as standard Verlet -timesteppnig, where only the coordinates are integrated and the -velocities are approximated as finite differences to the trajectories -(Ryckaert et al. (1977)). If the velocities are -integrated explicitly, as with velocity Verlet which is what LAMMPS -uses as an integration method, a second set of constraining forces is -required in order to eliminate velocity components along the bonds -(Andersen (1983)). -

    -

    In order to formulate individual constraints for SHAKE and RATTLE, -focus on a single molecule whose bonds are constrained. Let Ri and Vi -be the position and velocity of atom i at time n, for -i=1,...,N, where N is the number of sites of our reference -molecule. The distance vector between sites i and j is given by -

    -
    -
    -

    The constraints can then be formulated as -

    -
    -
    -

    The SHAKE algorithm satisfies the first condition, i.e. the sites at -time n+1 will have the desired separations Dij immediately after the -coordinates are integrated. If we also enforce the second condition, -the velocity components along the bonds will vanish. RATTLE satisfies -both conditions. As implemented in LAMMPS, fix rattle uses fix shake -for satisfying the coordinate constraints. Therefore the settings and -optional keywords are the same for both fixes, and all the information -below about SHAKE is also relevant for RATTLE. -

    -

    SHAKE: -

    -

    Each timestep the specified bonds and angles are reset to their -equilibrium lengths and angular values via the SHAKE algorithm -(Ryckaert et al. (1977)). This is done by applying an -additional constraint force so that the new positions preserve the -desired atom separations. The equations for the additional force are -solved via an iterative method that typically converges to an accurate -solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1 -part in 10000) and maximum # of iterations are specified as arguments. -Setting the N argument will print statistics to the screen and log -file about regarding the lengths of bonds and angles that are being -constrained. Small delta values mean SHAKE is doing a good job. -

    -

    In LAMMPS, only small clusters of atoms can be constrained. This is -so the constraint calculation for a cluster can be performed by a -single processor, to enable good parallel performance. A cluster is -defined as a central atom connected to others in the cluster by -constrained bonds. LAMMPS allows for the following kinds of clusters -to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or -one central atom bonded to 2 others and the angle between the 3 atoms -also constrained. This means water molecules or CH2 or CH3 groups may -be constrained, but not all the C-C backbone bonds of a long polymer -chain. -

    -

    The b constraint lists bond types that will be constrained. The t -constraint lists atom types. All bonds connected to an atom of the -specified type will be constrained. The m constraint lists atom -masses. All bonds connected to atoms of the specified masses will be -constrained (within a fudge factor of MASSDELTA specified in -fix_shake.cpp). The a constraint lists angle types. If both bonds -in the angle are constrained then the angle will also be constrained -if its type is in the list. -

    -

    For all constraints, a particular bond is only constrained if both -atoms in the bond are in the group specified with the SHAKE fix. -

    -

    The degrees-of-freedom removed by SHAKE bonds and angles are accounted -for in temperature and pressure computations. Similarly, the SHAKE -contribution to the pressure of the system (virial) is also accounted -for. -

    -

    IMPORTANT NOTE: This command works by using the current forces on -atoms to caculate an additional constraint force which when added will -leave the atoms in positions that satisfy the SHAKE constraints -(e.g. bond length) after the next time integration step. If you -define fixes (e.g. fix efield) that add additional -force to the atoms after fix shake operates, then this fix will not -take them into account and the time integration will typically not -satisfy the SHAKE constraints. The solution for this is to make sure -that fix shake is defined in your input script after any other fixes -which add or change forces (to atoms that fix shake operates on). -

    -
    - -

    The mol keyword should be used when other commands, such as fix -deposit or fix pour, add molecules -on-the-fly during a simulation, and you wish to contrain the new -molecules via SHAKE. You specify a template-ID previously defined -using the molecule command, which reads a file that -defines the molecule. You must use the same template-ID that the -command adding molecules uses. The coordinates, atom types, special -bond restrictions, and SHAKE info can be specified in the molecule -file. See the molecule command for details. The only -settings required to be in this file (by this command) are the SHAKE -info of atoms in the molecule. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    RATTLE: -

    -

    The velocity constraints lead to a linear system of equations which -can be solved analytically. The implementation of the algorithm in -LAMMPS closely follows (Andersen (1983)). -

    -

    IMPORTANT NOTE: The fix rattle command modifies forces and velocities -and thus should be defined after all other integration fixes in your -input script. If you define other fixes that modify velocities or -forces after fix rattle operates, then fix rattle will not take them -into account and the overall time integration will typically not -satisfy the RATTLE constraints. You can check whether the constraints -work correctly by setting the value of RATTLE_DEBUG in -src/fix_rattle.cpp to 1 and recompiling LAMMPS. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about these fixes is written to binary restart -files. None of the fix_modify options -are relevant to these fixes. No global or per-atom quantities are -stored by these fixes for access by various output -commands. No parameter of these fixes -can be used with the start/stop keywords of the run -command. These fixes are not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    These fixes are part of the RIGID package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    For computational efficiency, there can only be one shake or rattle -fix defined in a simulation. -

    -

    If you use a tolerance that is too large or a max-iteration count that -is too small, the constraints will not be enforced very strongly, -which can lead to poor energy conservation. You can test for this in -your system by running a constant NVE simulation with a particular set -of SHAKE parameters and monitoring the energy versus time. -

    -

    SHAKE or RATTLE should not be used to contrain an angle at 180 degrees -(e.g. linear CO2 molecule). This causes numeric difficulties. -

    -

    Related commands: none -

    -

    Default: none -

    -
    - - - -

    (Ryckaert) J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, -J of Comp Phys, 23, 327-341 (1977). -

    - - -

    (Andersen) H. Andersen, J of Comp Phys, 52, 24-34 (1983). -

    - diff --git a/doc/doc2/fix_smd.html b/doc/doc2/fix_smd.html deleted file mode 100644 index ececffdc41..0000000000 --- a/doc/doc2/fix_smd.html +++ /dev/null @@ -1,162 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix smd command -

    -

    Syntax: -

    -
    fix ID group-ID smd type values keyword values 
-
    -
    • ID, group-ID are documented in fix command - -
    • smd = style name of this fix command - -
    • mode = cvel or cfor to select constant velocity or constant force SMD - -
        cvel values = K vel
-    K = spring constant (force/distance units)
-    vel = velocity of pulling (distance/time units) 
-  cfor values = force
-    force = pulling force (force units) 
-
      -
    • keyword = tether or couple - -
        tether values = x y z R0
-    x,y,z = point to which spring is tethered
-    R0 = distance of end of spring from tether point (distance units)
-  couple values = group-ID2 x y z R0
-    group-ID2 = 2nd group to couple to fix group with a spring
-    x,y,z = direction of spring, automatically computed with 'auto'
-    R0 = distance of end of spring (distance units) 
-
      - -
    -

    Examples: -

    -
    fix  pull    cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
-fix  pull    cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
-fix  stretch cterm smd cvel 20.0  0.0001 couple nterm auto auto auto 0.0
-fix  pull    cterm smd cfor  5.0 tether 25.0 25.0 25.0 0.0 
-
    -

    Description: -

    -

    This fix implements several options of steered MD (SMD) as reviewed in -(Izrailev), which allows to induce conformational changes -in systems and to compute the potential of mean force (PMF) along the -assumed reaction coordinate (Park) based on Jarzynski's -equality (Jarzynski). This fix borrows a lot from fix -spring and fix setforce. -

    -

    You can apply a moving spring force to a group of atoms (tether -style) or between two groups of atoms (couple style). The spring -can then be used in either constant velocity (cvel) mode or in -constant force (cfor) mode to induce transitions in your systems. -When running in tether style, you may need some way to fix some -other part of the system (e.g. via fix -spring/self) -

    -

    The tether style attaches a spring between a point at a distance of -R0 away from a fixed point x,y,z and the center of mass of the fix -group of atoms. A restoring force of magnitude K (R - R0) Mi / M is -applied to each atom in the group where K is the spring constant, Mi -is the mass of the atom, and M is the total mass of all atoms in the -group. Note that K thus represents the total force on the group of -atoms, not a per-atom force. -

    -

    In cvel mode the distance R is incremented or decremented -monotonously according to the pulling (or pushing) velocity. -In cfor mode a constant force is added and the actual distance -in direction of the spring is recorded. -

    -

    The couple style links two groups of atoms together. The first -group is the fix group; the second is specified by group-ID2. The -groups are coupled together by a spring that is at equilibrium when -the two groups are displaced by a vector in direction x,y,z with -respect to each other and at a distance R0 from that displacement. -Note that x,y,z only provides a direction and will be internally -normalized. But since it represents the absolute displacement of -group-ID2 relative to the fix group, (1,1,0) is a different spring -than (-1,-1,0). For each vector component, the displacement can be -described with the auto parameter. In this case the direction is -recomputed in every step, which can be useful for steering a local -process where the whole object undergoes some other change. When the -relative positions and distance between the two groups are not in -equilibrium, the same spring force described above is applied to atoms -in each of the two groups. -

    -

    For both the tether and couple styles, any of the x,y,z values can -be specified as NULL which means do not include that dimension in the -distance calculation or force application. -

    -

    For constant velocity pulling (cvel mode), the running integral -over the pulling force in direction of the spring is recorded and -can then later be used to compute the potential of mean force (PMF) -by averaging over multiple independent trajectories along the same -pulling path. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    The fix stores the direction of the spring, current pulling target -distance and the running PMF to binary restart files. -See the read_restart command for info on how to -re-specify a fix in an input script that reads a restart file, so that -the operation of the fix continues in an uninterrupted fashion. -

    -

    None of the fix_modify options are relevant to this -fix. -

    -

    This fix computes a vector list of 7 quantities, which can be accessed -by various output commands. The -quantities in the vector are in this order: the x-, y-, and -z-component of the pulling force, the total force in direction of the -pull, the equilibrium distance of the spring, the distance between the -two reference points, and finally the accumulated PMF (the sum of -pulling forces times displacement). -

    -

    The force is the total force on the group of atoms by the spring. In -the case of the couple style, it is the force on the fix group -(group-ID) or the negative of the force on the 2nd group (group-ID2). -The vector values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix drag, fix spring, -fix spring/self, -fix spring/rg -

    -

    Default: none -

    -
    - - - -

    (Izrailev) Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, -Wriggers, Schulten. Computational Molecular Dynamics: Challenges, -Methods, Ideas, volume 4 of Lecture Notes in Computational Science and -Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998. -

    -

    (Park) -Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) -

    -

    (Jarzynski) -Jarzynski, Phys. Rev. Lett. 78, 2690 (1997) -

    - diff --git a/doc/doc2/fix_smd_adjust_dt.html b/doc/doc2/fix_smd_adjust_dt.html deleted file mode 100644 index e7fab431b1..0000000000 --- a/doc/doc2/fix_smd_adjust_dt.html +++ /dev/null @@ -1,63 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix smd/adjust_dt command -

    -

    Syntax: -

    -
    fix ID group-ID smd/adjust_dt arg 
-
    -
    • ID, group-ID are documented in fix command - -
    • smd/adjust_dt = style name of this fix command - -
    • arg = s_fact - -
        s_fact = safety factor  
-
      - -
    -

    Examples: -

    -
    fix 1 all smd/adjust_dt 0.1 
-
    -

    Description: -

    -

    The fix calculates a new stable time increment for use with the SMD time integrators. -

    -

    The stable time increment is based on multiple conditions. For the SPH pair styles, a -CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of -sound cannot propagate further than a typical spacing between particles within a single time step to ensure -no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a -stable maximum time step. -

    -

    This fix inquires the minimum stable time increment across all particles contained in the group for which this -fix is defined. An additional safety factor s_fact is applied to the time increment. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Currently, no part of USER-SMD supports restarting nor minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    smd/tlsph_dt -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_smd_integrate_tlsph.html b/doc/doc2/fix_smd_integrate_tlsph.html deleted file mode 100644 index f6a89384b4..0000000000 --- a/doc/doc2/fix_smd_integrate_tlsph.html +++ /dev/null @@ -1,59 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix smd/integrate_tlsph command -

    -

    Syntax: -

    -
    fix ID group-ID smd/integrate_tlsph keyword values 
-
    -
    • ID, group-ID are documented in fix command -
    • smd/integrate_tlsph = style name of this fix command -
    • zero or more keyword/value pairs may be appended -
    -
  • keyword = limit_velocity - -
      limit_velocity value = max_vel
-    max_vel = maximum allowed velocity 
-
    - - -

    Examples: -

    -
    fix 1 all smd/integrate_tlsph
-fix 1 all smd/integrate_tlsph limit_velocity 1000 
-
    -

    Description: -

    -

    The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    The limit_velocity keyword will control the velocity, scaling the norm of -the velocity vector to max_vel in case it exceeds this velocity limit. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    smd/integrate_ulsph -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_smd_integrate_ulsph.html b/doc/doc2/fix_smd_integrate_ulsph.html deleted file mode 100644 index 0ea578c2fc..0000000000 --- a/doc/doc2/fix_smd_integrate_ulsph.html +++ /dev/null @@ -1,63 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix smd/integrate_ulsph command -

    -

    Syntax: -

    -
    fix ID group-ID smd/integrate_ulsph keyword 
-
    -
    • ID, group-ID are documented in fix command -
    • smd/integrate_ulsph = style name of this fix command -
    • zero or more keyword/value pairs may be appended -
    -

    keyword = adjust_radius or limit_velocity -

    -

    adjust_radius values = adjust_radius_factor min_nn max_nn - adjust_radius_factor = factor which scale the smooth/kernel radius - min_nn = minimum number of neighbors - max_nn = maximum number of neighbors -limit_velocity values = max_velocity - max_velocity = maximum allowed velocity. -

    -

    Examples: -

    -
    fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 
-
    -
    fix 1 all smd/integrate_ulsph limit_velocity 1000 
-
    -

    Description: -

    -

    The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style. -See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    The adjust_radius keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains -within the interval min_nn to max_nn. The parameter adjust_radius_factor determines the amount of adjustment per timestep. Typical values are -adjust_radius_factor=1.02, min_nn=15, and max_nn=20. -

    -

    The limit_velocity keyword will control the velocity, scaling the norm of -the velocity vector to max_vel in case it exceeds this velocity limit. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_smd_move_triangulated_surface.html b/doc/doc2/fix_smd_move_triangulated_surface.html deleted file mode 100644 index e3d1cea464..0000000000 --- a/doc/doc2/fix_smd_move_triangulated_surface.html +++ /dev/null @@ -1,81 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix smd/move_tri_surf command -

    -

    Syntax: -

    -
    fix ID group-ID smd/move_tri_surf keyword 
-
    -
    • ID, group-ID are documented in fix command - -
    • smd/move_tri_surf keyword = style name of this fix command - -
    • keyword = *LINEAR or *WIGGLE or *ROTATE - -
         *LINEAR args = Vx Vy Vz
-      Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
-   *WIGGLE args = Vx Vy Vz max_travel
-      vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
-      max_travel = wiggle amplitude
-   *ROTATE args = Px Py Pz Rx Ry Rz period
-      Px,Py,Pz = origin point of axis of rotation (distance units)
-      Rx,Ry,Rz = axis of rotation vector
-      period = period of rotation (time units) 
-
      - -
    -

    Examples: -

    -
    fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
-fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
-fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 
-
    -

    Description: -

    -

    This fix applies only to rigid surfaces read from .STL files via fix smd/wall_surface . -It updates position and velocity for the particles in the group each timestep without regard to forces on the particles. -The rigid surfaces can thus be moved along simple trajectories during the simulation. -

    -

    The *LINEAR style moves particles with the specified constant velocity -vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle -to V = (Vx,Vy,Vz). -

    -

    The *WIGGLE style moves particles in an oscillatory fashion. -Particles are moved along (vx, vy, vz) with constant velocity until a -displacement of max_travel is reached. Then, the velocity vector is -reversed. This process is repeated. -

    -

    The *ROTATE style rotates particles around a rotation axis R = (Rx,Ry,Rz) that -goes through a point P = (Px,Py,Pz). The period of the rotation is also -specified. This style also sets the velocity of each particle to (omega cross -Rperp) where omega is its angular velocity around the rotation axis and -Rperp is a perpendicular vector from the rotation axis to the particle. -

    -

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    smd/triangle_mesh_vertices, smd/wall_surface -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_smd_setvel.html b/doc/doc2/fix_smd_setvel.html deleted file mode 100644 index 02124aa05a..0000000000 --- a/doc/doc2/fix_smd_setvel.html +++ /dev/null @@ -1,96 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix smd/setvel command -

    -

    Syntax: -

    -
    fix ID group-ID smd/setvel vx vy vz keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • smd/setvel = style name of this fix command - -
    • vx,vy,vz = velocity component values - -
    • any of vx,vy,vz can be a variable (see below) - -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = region - -
        region value = region-ID
-    region-ID = ID of region particles must be in to have their velocities set 
-
      - -
    -

    Examples: -

    -
    fix top_velocity top_group setvel 1.0 0.0 0.0 
-
    -

    Description: -

    -

    Set each component of velocity on each particle in the group to the specified -values vx,vy,vz, regardless of the forces acting on the particle. This command can -be used to impose velocity boundary conditions. -

    -

    Any of the vx,vy,vz values can be specified as NULL which means do not -alter the velocity component in that dimension. -

    -

    This fix is indented to be used together with a time integration fix. -

    -

    Any of the 3 quantities defining the velocity components can be specified -as an equal-style or atom-style variable, namely vx, -vy, vz. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -force component. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent velocity field. -

    -

    Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent velocity -field with optional time-dependence as well. -

    -

    If the region keyword is used, the particle must also be in the -specified geometric region in order to have its velocity set by this command. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Currently, no part of USER-SMD supports restarting nor minimization -None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global 3-vector of forces, which can be accessed -by various output commands. This is the -total force on the group of atoms. The vector values calculated by this -fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_smd_tlsph_reference_configuration.html b/doc/doc2/fix_smd_tlsph_reference_configuration.html deleted file mode 100644 index a0fa4f0f02..0000000000 --- a/doc/doc2/fix_smd_tlsph_reference_configuration.html +++ /dev/null @@ -1,2 +0,0 @@ - - diff --git a/doc/doc2/fix_smd_wall_surface.html b/doc/doc2/fix_smd_wall_surface.html deleted file mode 100644 index 8ddb59372c..0000000000 --- a/doc/doc2/fix_smd_wall_surface.html +++ /dev/null @@ -1,68 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix smd/wall_surface command -

    -

    Syntax: -

    -
    fix ID group-ID smd/wall_surface arg type mol-ID 
-
    -
    • ID, group-ID are documented in fix command - -
    • smd/wall_surface = style name of this fix command - -
    • arg = file - -
         file = file name of a triangular mesh in stl format 
-
      -
    • type = particle type to be given to the new particles created by this fix - -
    • mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) - - -
    -

    Examples: -

    -
    fix stl_surf all smd/wall_surface tool.stl 2 65535 
-
    -

    Description: -

    -

    This fix creates reads a traingulated surface from a file in .STL format. -For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions. -The radius of the new particle is that of the minimum circle which encompasses the triangle vertices. -

    -

    The triangulated surface can be used as a complex rigid wall via the smd/tri_surface pair style. -It is possible to move the triangulated surface via the smd/move_tri_surf fix style. -

    -

    Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles -in the system. See the "funnel_flow" example in the USER-SMD examples directory. -

    -

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. -

    -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535. -

    -

    Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file. -

    -

    Related commands: -

    -

    smd/triangle_mesh_vertices, smd/move_tri_surf, smd/tri_surface -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_spring.html b/doc/doc2/fix_spring.html deleted file mode 100644 index 80d6d695df..0000000000 --- a/doc/doc2/fix_spring.html +++ /dev/null @@ -1,151 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix spring command -

    -

    Syntax: -

    -
    fix ID group-ID spring keyword values 
-
    -
    • ID, group-ID are documented in fix command - -
    • spring = style name of this fix command - -
    • keyword = tether or couple - -
        tether values = K x y z R0
-    K = spring constant (force/distance units)
-    x,y,z = point to which spring is tethered
-    R0 = equilibrium distance from tether point (distance units)
-  couple values = group-ID2 K x y z R0
-    group-ID2 = 2nd group to couple to fix group with a spring
-    K = spring constant (force/distance units)
-    x,y,z = direction of spring
-    R0 = equilibrium distance of spring (distance units) 
-
      - -
    -

    Examples: -

    -
    fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0
-fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0
-fix pull ligand spring tether 50.0 NULL NULL 2.0 3.0
-fix 5 bilayer1 spring couple bilayer2 100.0 NULL NULL 10.0 0.0
-fix longitudinal pore spring couple ion 100.0 NULL NULL -20.0 0.0
-fix radial pore spring couple ion 100.0 0.0 0.0 NULL 5.0 
-
    -

    Description: -

    -

    Apply a spring force to a group of atoms or between two groups of -atoms. This is useful for applying an umbrella force to a small -molecule or lightly tethering a large group of atoms (e.g. all the -solvent or a large molecule) to the center of the simulation box so -that it doesn't wander away over the course of a long simulation. It -can also be used to hold the centers of mass of two groups of atoms at -a given distance or orientation with respect to each other. -

    -

    The tether style attaches a spring between a fixed point x,y,z and -the center of mass of the fix group of atoms. The equilibrium -position of the spring is R0. At each timestep the distance R from -the center of mass of the group of atoms to the tethering point is -computed, taking account of wrap-around in a periodic simulation box. -A restoring force of magnitude K (R - R0) Mi / M is applied to each -atom in the group where K is the spring constant, Mi is the mass of -the atom, and M is the total mass of all atoms in the group. Note -that K thus represents the total force on the group of atoms, not a -per-atom force. -

    -

    The couple style links two groups of atoms together. The first -group is the fix group; the second is specified by group-ID2. The -groups are coupled together by a spring that is at equilibrium when -the two groups are displaced by a vector x,y,z with respect to each -other and at a distance R0 from that displacement. Note that x,y,z -is the equilibrium displacement of group-ID2 relative to the fix -group. Thus (1,1,0) is a different spring than (-1,-1,0). When the -relative positions and distance between the two groups are not in -equilibrium, the same spring force described above is applied to atoms -in each of the two groups. -

    -

    For both the tether and couple styles, any of the x,y,z values can -be specified as NULL which means do not include that dimension in the -distance calculation or force application. -

    -

    The first example above pulls the ligand towards the point (0,0,0). -The second example holds the ligand near the surface of a sphere of -radius 5 around the point (0,0,0). The third example holds the ligand -a distance 3 away from the z=2 plane (on either side). -

    -

    The fourth example holds 2 bilayers a distance 10 apart in z. For the -last two examples, imagine a pore (a slab of atoms with a cylindrical -hole cut out) oriented with the pore axis along z, and an ion moving -within the pore. The fifth example holds the ion a distance of -20 -below the z = 0 center plane of the pore (umbrella sampling). The -last example holds the ion a distance 5 away from the pore axis -(assuming the center-of-mass of the pore in x,y is the pore axis). -

    -

    IMPORTANT NOTE: The center of mass of a group of atoms is calculated -in "unwrapped" coordinates using atom image flags, which means that -the group can straddle a periodic boundary. See the dump -doc page for a discussion of unwrapped coordinates. It also means -that a spring connecting two groups or a group and the tether point -can cross a periodic boundary and its length be calculated correctly. -One exception is for rigid bodies, which should not be used with the -fix spring command, if the rigid body will cross a periodic boundary. -This is because image flags for rigid bodies are used in a different -way, as explained on the fix rigid doc page. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the energy stored in the spring to the system's potential -energy as part of thermodynamic output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -spring energy = 0.5 * K * r^2. -

    -

    This fix also computes global 4-vector which can be accessed by -various output commands. The first 3 -quantities in the vector are xyz components of the total force added -to the group of atoms by the spring. In the case of the couple -style, it is the force on the fix group (group-ID) or the negative of -the force on the 2nd group (group-ID2). The 4th quantity in the -vector is the magnitude of the force added by the spring, as a -positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This -sign convention can be useful when using the spring force to compute a -potential of mean force (PMF). -

    -

    The scalar and vector values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    IMPORTANT NOTE: If you want the spring energy to be included in the -total potential energy of the system (the quantity being minimized), -you MUST enable the fix_modify energy option for -this fix. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix drag, fix spring/self, -fix spring/rg, fix smd -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_spring_rg.html b/doc/doc2/fix_spring_rg.html deleted file mode 100644 index 535e088be6..0000000000 --- a/doc/doc2/fix_spring_rg.html +++ /dev/null @@ -1,72 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix spring/rg command -

    -

    Syntax: -

    -
    fix ID group-ID spring/rg K RG0 
-
    -
    • ID, group-ID are documented in fix command -
    • spring/rg = style name of this fix command -
    • K = harmonic force constant (force/distance units) -
    • RG0 = target radius of gyration to constrain to (distance units) -
    -
      if RG0 = NULL, use the current RG as the target value 
-
    -

    Examples: -

    -
    fix 1 protein spring/rg 5.0 10.0
-fix 2 micelle spring/rg 5.0 NULL 
-
    -

    Description: -

    -

    Apply a harmonic restraining force to atoms in the group to affect -their central moment about the center of mass (radius of gyration). -This fix is useful to encourage a protein or polymer to fold/unfold -and also when sampling along the radius of gyration as a reaction -coordinate (i.e. for protein folding). -

    -

    The radius of gyration is defined as RG in the first formula. The -energy of the constraint and associated force on each atom is given by -the second and third formulas, when the group is at a different RG -than the target value RG0. -

    -
    -
    -

    The (xi - center-of-mass) term is computed taking into account -periodic boundary conditions, m_i is the mass of the atom, and M is -the mass of the entire group. Note that K is thus a force constant -for the aggregate force on the group of atoms, not a per-atom force. -

    -

    If RG0 is specified as NULL, then the RG of the group is computed at -the time the fix is specified, and that value is used as the target. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix spring, fix spring/self -fix drag, fix smd -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_spring_self.html b/doc/doc2/fix_spring_self.html deleted file mode 100644 index 7665abdddf..0000000000 --- a/doc/doc2/fix_spring_self.html +++ /dev/null @@ -1,84 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix spring/self command -

    -

    Syntax: -

    -
    fix ID group-ID spring/self K dir 
-
    -
    • ID, group-ID are documented in fix command -
    • spring/self = style name of this fix command -
    • K = spring constant (force/distance units) -
    • dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz) -
    -

    Examples: -

    -
    fix tether boundary-atoms spring/self 10.0
-fix zrest  move spring/self 10.0 z 
-
    -

    Description: -

    -

    Apply a spring force independently to each atom in the group to tether -it to its initial position. The initial position for each atom is its -location at the time the fix command was issued. At each timestep, -the magnitude of the force on each atom is -Kr, where r is the -displacement of the atom from its current position to its initial -position. The distance r correctly takes into account any crossings -of periodic boundary by the atom since it was in its intitial -position. -

    -

    With the (optional) dir flag, one can select in which direction the -spring force is applied. By default, the restraint is applied in all -directions, but it can be limited to the xy-, xz-, yz-plane and the -x-, y-, or z-direction, thus restraining the atoms to a line or a -plane, respectively. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the original coordinates of tethered atoms to binary -restart files, so that the spring effect will be the -same in a restarted simulation. See the -read_restart command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. -

    -

    The fix_modify energy option is supported by this -fix to add the energy stored in the per-atom springs to the system's -potential energy as part of thermodynamic output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is an -energy which is the sum of the spring energy for each atom, where the -per-atom energy is 0.5 * K * r^2. The scalar value calculated by this -fix is "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    IMPORTANT NOTE: If you want the per-atom spring energy to be included -in the total potential energy of the system (the quantity being -minimized), you MUST enable the fix_modify energy -option for this fix. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix drag, fix spring, -fix smd, fix spring/rg -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_srd.html b/doc/doc2/fix_srd.html deleted file mode 100644 index 9c87160d74..0000000000 --- a/doc/doc2/fix_srd.html +++ /dev/null @@ -1,410 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix srd command -

    -

    Syntax: -

    -
    fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ... 
-
    -
    • ID, group-ID are documented in fix command -
    • srd = style name of this fix command -
    • N = reset SRD particle velocities every this many timesteps -
    • groupbig-ID = ID of group of large particles that SRDs interact with -
    • Tsrd = temperature of SRD particles (temperature units) -
    • hgrid = grid spacing for SRD grouping (distance units) -
    • seed = random # seed (positive integer) -
    -
    • zero or more keyword/value pairs may be appended - -
    • keyword = lamda or collision or overlap or inside or exact or radius or bounce or search or cubic or shift or tstat or rescale - -
        lamda value = mean free path of SRD particles (distance units)
-  collision value = noslip or slip = collision model
-  overlap value = yes or no = whether big particles may overlap
-  inside value = error or warn or ignore = how SRD particles which end up inside a big particle are treated
-  exact value = yes or no
-  radius value = rfactor = scale collision radius by this factor
-  bounce value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
-  search value = sgrid = grid spacing for collision partner searching (distance units)
-  cubic values = style tolerance
-    style = error or warn
-    tolerance = fractional difference allowed (0 <= tol <= 1)
-  shift values = flag shiftseed
-    flag = yes or no or possible = SRD bin shifting for better statistics
-      yes = perform bin shifting each time SRD velocities are rescaled
-      no = no shifting
-      possible = shift depending on mean free path and bin size
-    shiftseed = random # seed (positive integer)
-  tstat value = yes or no = thermostat SRD particles or not
-  rescale value = yes or no or rotate or collide = rescaling of SRD velocities
-    yes = rescale during velocity rotation and collisions
-    no = no rescaling
-    rotate = rescale during velocity rotation, but not collisions
-    collide = rescale during collisions, but not velocity rotation 
-
      - -
    -

    Examples: -

    -
    fix 1 srd srd 10 big 1.0 0.25 482984
-fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5 
-
    -

    Description: -

    -

    Treat a group of partilces as stochastic rotation dynamics (SRD) -particles that serve as a background solvent when interacting with big -(colloidal) particles in groupbig-ID. The SRD formalism is described -in (Hecht). The key idea behind using SRD particles as a -cheap coarse-grained solvent is that SRD particles do not interact -with each other, but only with the solute particles, which in LAMMPS -can be spheroids, ellipsoids, or line segments, or triangles, or rigid -bodies containing multiple spherioids or ellipsoids or line segments -or triangles. The collision and rotation properties of the model -imbue the SRD particles with fluid-like properties, including an -effective viscosity. Thus simulations with large solute particles can -be run more quickly, to measure solute propoerties like diffusivity -and viscosity in a background fluid. The usual LAMMPS fixes for such -simulations, such as fix deform, fix -viscosity, and fix nvt/sllod, -can be used in conjunction with the SRD model. -

    -

    For more details on how the SRD model is implemented in LAMMPS, this -paper describes the implementation and usage of pure SRD -fluids. This paper, which is nearly complete, describes -the implementation and usage of mixture systems (solute particles in -an SRD fluid). See the examples/srd directory for sample input -scripts using SRD particles in both settings. -

    -

    This fix does 2 things: -

    -

    (1) It advects the SRD particles, performing collisions between SRD -and big particles or walls every timestep, imparting force and torque -to the big particles. Collisions also change the position and -velocity of SRD particles. -

    -

    (2) It resets the velocity distribution of SRD particles via random -rotations every N timesteps. -

    -

    SRD particles have a mass, temperature, characteristic timestep -dt_SRD, and mean free path between collisions (lamda). The -fundamental equation relating these 4 quantities is -

    -
    lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) 
-
    -

    The mass of SRD particles is set by the mass command -elsewhere in the input script. The SRD timestep dt_SRD is N times the -step dt defined by the timestep command. Big -particles move in the normal way via a time integration fix -with a short timestep dt. SRD particles advect with a large timestep -dt_SRD >= dt. -

    -

    If the lamda keyword is not specified, the the SRD temperature -Tsrd is used in the above formula to compute lamda. If the lamda -keyword is specified, then the Tsrd setting is ignored and the above -equation is used to compute the SRD temperature. -

    -

    The characteristic length scale for the SRD fluid is set by hgrid -which is used to bin SRD particles for purposes of resetting their -velocities. Normally hgrid is set to be 1/4 of the big particle -diameter or smaller, to adequately resolve fluid properties around the -big particles. -

    -

    Lamda cannot be smaller than 0.6 * hgrid, else an error is generated -(unless the shift keyword is used, see below). The velocities of -SRD particles are bounded by Vmax, which is set so that an SRD -particle will not advect further than Dmax = 4*lamda in dt_SRD. This -means that roughly speaking, Dmax should not be larger than a big -particle diameter, else SRDs may pass thru big particles without -colliding. A warning is generated if this is the case. -

    -

    Collisions between SRD particles and big particles or walls are -modeled as a lightweight SRD point particle hitting a heavy big -particle of given diameter or a wall at a point on its surface and -bouncing off with a new velocity. The collision changes the momentum -of the SRD particle. It imparts a force and torque to the big -particle. It imparts a force to a wall. Static or moving SRD walls -are setup via the fix wall/srd command. For the -remainder of this doc page, a collision of an SRD particle with a wall -can be viewed as a collision with a big particle of infinite radius -and mass. -

    -

    The collision keyword sets the style of collisions. The slip -style means that the tangential component of the SRD particle momentum -is preserved. Thus a force is imparted to a big particle, but no -torque. The normal component of the new SRD velocity is sampled from -a Gaussian distribution at temperature Tsrd. -

    -

    For the noslip style, both the normal and tangential components of -the new SRD velocity are sampled from a Gaussian distribution at -temperature Tsrd. Additionally, a new tangential direction for the -SRD velocity is chosen randomly. This collision style imparts torque -to a big particle. Thus a time integrator fix that rotates -the big particles appropriately should be used. -

    -
    - -

    The overlap keyword should be set to yes if two (or more) big -particles can ever overlap. This depends on the pair potential -interaction used for big-big interactions, or could be the case if -multiple big particles are held together as rigid bodies via the fix -rigid command. If the overlap keyword is no and -big particles do in fact overlap, then SRD/big collisions can generate -an error if an SRD ends up inside two (or more) big particles at once. -How this error is treated is determined by the inside keyword. -Running with overlap set to no allows for faster collision -checking, so it should only be set to yes if needed. -

    -

    The inside keyword determines how a collision is treated if the -computation determines that the timestep started with the SRD particle -already inside a big particle. If the setting is error then this -generates an error message and LAMMPS stops. If the setting is warn -then this generates a warning message and the code continues. If the -setting is ignore then no message is generated. One of the output -quantities logged by the fix (see below) tallies the number of such -events, so it can be monitored. Note that once an SRD particle is -inside a big particle, it may remain there for several steps until it -drifts outside the big particle. -

    -

    The exact keyword determines how accurately collisions are computed. -A setting of yes computes the time and position of each collision as -SRD and big particles move together. A setting of no estimates the -position of each collision based on the end-of-timestep positions of -the SRD and big particle. If overlap is set to yes, the setting of -the exact keyword is ignored since time-accurate collisions are -needed. -

    -

    The radius keyword scales the effective size of big particles. If -big particles will overlap as they undergo dynamics, then this keyword -can be used to scale down their effective collision radius by an -amount rfactor, so that SRD particle will only collide with one big -particle at a time. For example, in a Lennard-Jones system at a -temperature of 1.0 (in reduced LJ units), the minimum separation -bewteen two big particles is as small as about 0.88 sigma. Thus an -rfactor value of 0.85 should prevent dual collisions. -

    -

    The bounce keyword can be used to limit the maximum number of -collisions an SRD particle undergoes in a single timestep as it -bounces between nearby big particles. Note that if the limit is -reached, the SRD can be left inside a big particle. A setting of 0 is -the same as no limit. -

    -
    - -

    There are 2 kinds of bins created and maintained when running an SRD -simulation. The first are "SRD bins" which are used to bin SRD -particles and reset their velocities, as discussed above. The second -are "search bins" which are used to identify SRD/big particle -collisions. -

    -

    The search keyword can be used to choose a search bin size for -identifying SRD/big particle collisions. The default is to use the -hgrid parameter for SRD bins as the search bin size. Choosing a -smaller or large value may be more efficient, depending on the -problem. But, in a statistical sense, it should not change the -simulation results. -

    -

    The cubic keyword can be used to generate an error or warning when -the bin size chosen by LAMMPS creates SRD bins that are non-cubic or -different than the requested value of hgrid by a specified -tolerance. Note that using non-cubic SRD bins can lead to -undetermined behavior when rotating the velocities of SRD particles, -hence LAMMPS tries to protect you from this problem. -

    -

    LAMMPS attempts to set the SRD bin size to exactly hgrid. However, -there must be an integer number of bins in each dimension of the -simulation box. Thus the actual bin size will depend on the size and -shape of the overall simulation box. The actual bin size is printed -as part of the SRD output when a simulation begins. -

    -

    If the actual bin size in non-cubic by an amount exceeding the -tolerance, an error or warning is printed, depending on the style of -the cubic keyword. Likewise, if the actual bin size differs from -the requested hgrid value by an amount exceeding the tolerance, then -an error or warning is printed. The tolerance is a fractional -difference. E.g. a tolerance setting of 0.01 on the shape means that -if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an -error or warning is generated. Similarly, if the ratio of any bin -dimension with hgrid exceeds (1 +/- tolerance), then an error or -warning is generated. -

    -

    IMPORTANT NOTE: The fix srd command can be used with simluations the -size and/or shape of the simulation box changes. This can be due to -non-periodic boundary conditions or the use of fixes such as the fix -deform or fix wall/srd commands -to impose a shear on an SRD fluid or an interaction with an external -wall. If the box size changes then the size of SRD bins must be -recalculated every reneighboring. This is not necessary if only the -box shape changes. This re-binning is always done so as to fit an -integer number of bins in the current box dimension, whether it be a -fixed, shrink-wrapped, or periodic boundary, as set by the -boundary command. If the box size or shape changes, -then the size of the search bins must be recalculated avery -reneighboring. Note that changing the SRD bin size may alter the -properties of the SRD fluid, such as its viscosity. -

    -

    The shift keyword determines whether the coordinates of SRD -particles are randomly shifted when binned for purposes of rotating -their velocities. When no shifting is performed, SRD particles are -binned and the velocity distribution of the set of SRD particles in -each bin is adjusted via a rotation operator. This is a statistically -valid operation if SRD particles move sufficiently far between -successive rotations. This is determined by their mean-free path -lamda. If lamda is less than 0.6 of the SRD bin size, then shifting -is required. A shift means that all of the SRD particles are shifted -by a vector whose coordinates are chosen randomly in the range [-1/2 -bin size, 1/2 bin size]. Note that all particles are shifted by the -same vector. The specified random number shiftseed is used to -generate these vectors. This operation sufficiently randomizes which -SRD particles are in the same bin, even if lamda is small. -

    -

    If the shift flag is set to no, then no shifting is performed, but -bin data will be communicated if bins overlap processor boundaries. -An error will be generated if lamda < 0.6 of the SRD bin size. If the -shift flag is set to possible, then shifting is performed only if -lamda < 0.6 of the SRD bin size. A warning is generated to let you -know this is occurring. If the shift flag is set to yes then -shifting is performed regardless of the magnitude of lamda. Note that -the shiftseed is not used if the shift flag is set to no, but -must still be specified. -

    -

    Note that shifting of SRD coordinates requires extra communication, -hence it should not normally be enabled unless required. -

    -

    The tstat keyword will thermostat the SRD particles to the specified -Tsrd. This is done every N timesteps, during the velocity rotation -operation, by rescaling the thermal velocity of particles in each SRD -bin to the desired temperature. If there is a streaming velocity -associated with the system, e.g. due to use of the fix -deform command to perform a simulation undergoing -shear, then that is also accounted for. The mean velocity of each bin -of SRD particles is set to the position-dependent streaming velocity, -based on the coordinates of the center of the SRD bin. Note that -collisions of SRD particles with big particles or walls has a -thermostatting effect on the colliding particles, so it may not be -necessary to thermostat the SRD particles on a bin by bin basis in -that case. Also note that for streaming simulations, if no -thermostatting is performed (the default), then it may take a long -time for the SRD fluid to come to equilibrium with a velocity profile -that matches the simulation box deformation. -

    -

    The rescale keyword enables rescaling of an SRD particle's velocity -if it would travel more than 4 mean-free paths in an SRD timestep. If -an SRD particle exceeds this velocity it is possible it will be lost -when migrating to other processors or that collisions with big -particles will be missed, either of which will generate errors. Thus -the safest mode is to run with rescaling enabled. However rescaling -removes kinetic energy from the system (the particle's velocity is -reduced). The latter will not typically be a problem if -thermostatting is enabled via the tstat keyword or if SRD collisions -with big particles or walls effectively thermostat the system. If you -wish to turn off rescaling (on is the default), e.g. for a pure SRD -system with no thermostatting so that the temperature does not decline -over time, the rescale keyword can be used. The no value turns -rescaling off during collisions and the per-bin velocity rotation -operation. The collide and rotate values turn it on for -one of the operations and off for the other. -

    -
    - -

    IMPORTANT NOTE: This fix is normally used for simulations with a huge -number of SRD particles relative to the number of big particles, -e.g. 100 to 1. In this scenario, computations that involve only big -particles (neighbor list creation, communication, time integration) -can slow down dramatically due to the large number of background SRD -particles. -

    -

    Three other input script commands will largely overcome this effect, -speeding up an SRD simulation by a significant amount. These are the -atom_modify first, neigh_modify -include, and comm_modify group -commands. Each takes a group-ID as an argument, which in this case -should be the group-ID of the big solute particles. -

    -

    Additionally, when a pair_style for big/big particle -interactions is specified, the pair_coeff command -should be used to turn off big/SRD interactions, e.g. by setting their -epsilon or cutoff length to 0.0. -

    -

    The "delete_atoms overlap" command may be useful in setting up an SRD -simulation to insure there are no initial overlaps between big and SRD -particles. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix tabulates several SRD statistics which are stored in a vector -of length 12, which can be accessed by various output -commands. The vector values calculated -by this fix are "intensive", meaning they do not scale with the size -of the simulation. Technically, the first 8 do scale with the size of -the simulation, but treating them as intensive means they are not -scaled when printed as part of thermodyanmic output. -

    -

    These are the 12 quantities. All are values for the current timestep, -except for quantity 5 and the last three, each of which are -cummulative quantities since the beginning of the run. -

    -
    • (1) # of SRD/big collision checks performed -
    • (2) # of SRDs which had a collision -
    • (3) # of SRD/big colllisions (including multiple bounces) -
    • (4) # of SRD particles inside a big particle -
    • (5) # of SRD particles whose velocity was rescaled to be < Vmax -
    • (6) # of bins for collision searching -
    • (7) # of bins for SRD velocity rotation -
    • (8) # of bins in which SRD temperature was computed -
    • (9) SRD temperature -
    • (10) # of SRD particles which have undergone max # of bounces -
    • (11) max # of bounces any SRD particle has had in a single step -
    • (12) # of reneighborings due to SRD particles moving too far -
    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This command can only be used if LAMMPS was built with the SRD -package. See the Making LAMMPS section -for more info on packages. -

    -

    Related commands: -

    -

    fix wall/srd -

    -

    Default: -

    -

    The option defaults are lamda inferred from Tsrd, collision = noslip, -overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0, -search = hgrid, cubic = error 0.01, shift = no, tstat = no, and -rescale = yes. -

    -
    - - - -

    (Hecht) Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005). -

    - - -

    (Petersen) Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J -Chem Phys, 132, 174106 (2010). -

    - - -

    (Lechman) Lechman, et al, in preparation (2010). -

    - diff --git a/doc/doc2/fix_store_force.html b/doc/doc2/fix_store_force.html deleted file mode 100644 index f73bdf65b9..0000000000 --- a/doc/doc2/fix_store_force.html +++ /dev/null @@ -1,77 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix store/force command -

    -

    Syntax: -

    -
    fix ID group-ID store/force 
-
    -
    • ID, group-ID are documented in fix command -
    • store/force = style name of this fix command -
    -

    Examples: -

    -
    fix 1 all store/force 
-
    -

    Description: -

    -

    Store the forces on atoms in the group at the point during each -timestep when the fix is invoked, as described below. This is useful -for storing forces before constraints or other boundary conditions are -computed which modify the forces, so that unmodified forces can be -written to a dump file or accessed by other output -commands that use per-atom quantities. -

    -

    This fix is invoked at the point in the velocity-Verlet timestepping -immediately after pair, bond, -angle, dihedral, -improper, and long-range -forces have been calculated. It is the point in the timestep when -various fixes that compute constraint forces are calculated and -potentially modify the force on each atom. Examples of such fixes are -fix shake, fix wall, and fix -indent. -

    -

    IMPORTANT NOTE: The order in which various fixes are applied which -operate at the same point during the timestep, is the same as the -order they are specified in the input script. Thus normally, if you -want to store per-atom forces due to force field interactions, before -constraints are applied, you should list this fix first within that -set of fixes, i.e. before other fixes that apply constraints. -However, if you wish to include certain constraints (e.g. fix shake) -in the stored force, then it could be specified after some fixes and -before others. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix produces a per-atom array which can be accessed by various -output commands. The number of columns -for each atom is 3, and the columns store the x,y,z forces on each -atom. The per-atom values be accessed on any timestep. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix store_state -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_store_state.html b/doc/doc2/fix_store_state.html deleted file mode 100644 index 641dbf7eae..0000000000 --- a/doc/doc2/fix_store_state.html +++ /dev/null @@ -1,143 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix store/state command -

    -

    Syntax: -

    -
    fix ID group-ID store/state N input1 input2 ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • store/state = style name of this fix command - -
    • N = store atom attributes every N steps, N = 0 for initial store only - -
    • input = one or more atom attributes - -
        possible attributes = id, mol, type, mass,
- 	                x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-		        vx, vy, vz, fx, fy, fz,
-                        q, mux, muy, muz,
-                        radius, omegax, omegay, omegaz,
-                        angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                        c_ID, c_ID[N], f_ID, f_ID[N], v_name,
-                        d_name, i_name 
-
      -
            id = atom ID
-      mol = molecule ID
-      type = atom type
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipolar atom
-      radius = radius of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      tqx,tqy,tqz = torque on finite-size particles
-      c_ID = per-atom vector calculated by a compute with ID
-      c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-      f_ID = per-atom vector calculated by a fix with ID
-      f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-      v_name = per-atom vector calculated by an atom-style variable with name
-      d_name = per-atom floating point vector name, managed by fix property/atom
-      i_name = per-atom integer vector name, managed by fix property/atom 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = com - -
        com value = yes or no 
-
      - -
    -

    Examples: -

    -
    fix 1 all store/state 0 x y z
-fix 1 all store/state 0 xu yu zu com yes
-fix 2 all store/state 1000 vx vy vz 
-
    -

    Description: -

    -

    Define a fix that stores attributes for each atom in the group at the -time the fix is defined. If N is 0, then the values are never -updated, so this is a way of archiving an atom attribute at a given -time for future use in a calculation or output. See the discussion of -output commands that take fixes as -inputs. And see for example, the compute -reduce, fix ave/atom, fix -ave/histo, fix ave/spatial, -and atom-style variable commands. -

    -

    If N is not zero, then the attributes will be updated every N -steps. -

    -

    IMPORTANT NOTE: Actually, only atom attributes specified by keywords -like xu or vy are initially stored immediately at the point in -your input script when the fix is defined. Attributes specified by a -compute, fix, or variable are not initially stored until the first run -following the fix definition begins. This is because calculating -those attributes may require quantities that are not defined in -between runs. -

    -

    The list of possible attributes is the same as that used by the dump -custom command, which describes their meaning. -

    -

    If the com keyword is set to yes then the xu, yu, and zu -inputs store the position of each atom relative to the center-of-mass -of the group of atoms, instead of storing the absolute position. This -option is used by the compute msd command. -

    -

    The requested values are stored in a per-atom vector or array as -discussed below. Zeroes are stored for atoms not in the specified -group. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the per-atom values it stores to binary restart -files, so that the values can be restored when a -simulation is restarted. See the read_restart -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    None of the fix_modify options are relevant to this -fix. -

    -

    If a single input is specified, this fix produces a per-atom vector. -If multiple inputs are specified, a per-atom array is produced where -the number of columns for each atom is the number of inputs. These -can be accessed by various output -commands. The per-atom values be -accessed on any timestep. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump custom, compute -property/atom, -fix property/atom, variable -

    -

    Default: -

    -

    The option default is com = no. -

    - diff --git a/doc/doc2/fix_temp_berendsen.html b/doc/doc2/fix_temp_berendsen.html deleted file mode 100644 index 6ae3f4ed9a..0000000000 --- a/doc/doc2/fix_temp_berendsen.html +++ /dev/null @@ -1,190 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix temp/berendsen command -

    -

    fix temp/berendsen/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID temp/berendsen Tstart Tstop Tdamp 
-
    -
    • ID, group-ID are documented in fix command - -
    • temp/berendsen = style name of this fix command - -
    • Tstart,Tstop = desired temperature at start/end of run - -
        Tstart can be a variable (see below) 
-
      -
    • Tdamp = temperature damping parameter (time units) -
    -

    Examples: -

    -
    fix 1 all temp/berendsen 300.0 300.0 100.0 
-
    -

    Description: -

    -

    Reset the temperature of a group of atoms by using a Berendsen -thermostat (Berendsen), which rescales their velocities -every timestep. -

    -

    The thermostat is applied to only the translational degrees of freedom -for the particles, which is an important consideration for finite-size -particles which have rotational degrees of freedom are being -thermostatted with this fix. The translational degrees of freedom can -also have a bias velocity removed from them before thermostatting -takes place; see the description below. -

    -

    The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The Tdamp parameter is specified in -time units and determines how rapidly the temperature is relaxed. For -example, a value of 100.0 means to relax the temperature in a timespan -of (roughly) 100 time units (tau or fmsec or psec - see the -units command). -

    -

    Tstart can be specified as an equal-style variable. -In this case, the Tstop setting is ignored. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the target temperature. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. -

    -

    IMPORTANT NOTE: Unlike the fix nvt command which -performs Nose/Hoover thermostatting AND time integration, this fix -does NOT perform time integration. It only modifies velocities to -effect thermostatting. Thus you must use a separate time integration -fix, like fix nve to actually update the positions of -atoms using the modified velocities. Likewise, this fix should not -normally be used on atoms that also have their temperature controlled -by another fix - e.g. by fix nvt or fix -langevin commands. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp", as if this command had been -issued: -

    -
    compute fix-ID_temp group-ID temp 
-
    -

    See the compute temp command for details. Note -that the ID of the new compute is the fix-ID + underscore + "temp", -and the group for the new compute is the same as the fix group. -

    -

    Note that this is NOT the compute used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -compute_modify command or print this temperature -during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp will have no -effect on this fix. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a temperature compute -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change implied by a velocity rescaling to the -system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix can be used with dynamic groups as defined by the -group command. Likewise it can be used with groups to -which atoms are added or deleted over time, e.g. a deposition -simulation. However, the conservation properties of the thermostat -and barostat are defined for systems with a static set of atoms. You -may observe odd behavior if the atoms in a group vary dramatically -over time or the atom count becomes very small. -

    -

    Related commands: -

    -

    fix nve, fix nvt, fix -temp/rescale, fix langevin, -fix_modify, compute temp, -fix press/berendsen -

    -

    Default: none -

    -
    - - - -

    (Berendsen) Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem -Phys, 81, 3684 (1984). -

    - diff --git a/doc/doc2/fix_temp_csvr.html b/doc/doc2/fix_temp_csvr.html deleted file mode 100644 index 41c6e7400e..0000000000 --- a/doc/doc2/fix_temp_csvr.html +++ /dev/null @@ -1,182 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix temp/csvr command -

    -

    fix temp/csld command -

    -

    Syntax: -

    -
    fix ID group-ID temp/csvr Tstart Tstop Tdamp seed 
-
    -
    fix ID group-ID temp/csld Tstart Tstop Tdamp seed 
-
    -
    • ID, group-ID are documented in fix command - -
    • temp/csvr or temp/csld = style name of this fix command - -
    • Tstart,Tstop = desired temperature at start/end of run - -
        Tstart can be a variable (see below) 
-
      -
    • Tdamp = temperature damping parameter (time units) - -
    • seed = random number seed to use for white noise (positive integer) -
    -

    Examples: -

    -
    fix 1 all temp/csvr 300.0 300.0 100.0 54324 
-
    -
    fix 1 all temp/csld 100.0 300.0 10.0 123321 
-
    -

    Description: -

    -

    Adjust the temperature with a canonical sampling thermostat that uses -global velocity rescaling with Hamiltonian dynamics (temp/csvr) -(Bussi1), or Langevin dynamics (temp/csld) -(Bussi2). In the case of temp/csvr the thermostat is -similar to the empirical Berendsen thermostat in -temp/berendsen, but chooses the actual -scaling factor from a suitably chosen (gaussian) distribution rather -than having it determined from the time constant directly. In the case -of temp/csld the velocities are updated to a linear combination of -the current velocities with a gaussian distribution of velocities at -the desired temperature. Both termostats are applied every timestep. -

    -

    The thermostat is applied to only the translational degrees of freedom -for the particles, which is an important consideration for finite-size -particles which have rotational degrees of freedom are being -thermostatted with these fixes. The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. -

    -

    The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The Tdamp parameter is specified in -time units and determines how rapidly the temperature is relaxed. For -example, a value of 100.0 means to relax the temperature in a timespan -of (roughly) 100 time units (tau or fmsec or psec - see the -units command). -

    -

    Tstart can be specified as an equal-style variable. -In this case, the Tstop setting is ignored. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the target temperature. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. -

    -

    IMPORTANT NOTE: Unlike the fix nvt command which -performs Nose/Hoover thermostatting AND time integration, these fixes -do NOT perform time integration. They only modify velocities to effect -thermostatting. Thus you must use a separate time integration fix, -like fix nve to actually update the positions of atoms -using the modified velocities. Likewise, these fixes should not -normally be used on atoms that also have their temperature controlled -by another fix - e.g. by fix nvt or fix -langevin commands. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    These fixes compute a temperature each timestep. To do this, the fix -creates its own compute of style "temp", as if this command had been -issued: -

    -
    compute fix-ID_temp group-ID temp 
-
    -

    See the compute temp command for details. Note -that the ID of the new compute is the fix-ID + underscore + "temp", -and the group for the new compute is the same as the fix group. -

    -

    Note that this is NOT the compute used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -compute_modify command or print this temperature -during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp will have no -effect on this fix. -

    -

    Like other fixes that perform thermostatting, these fixes can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about these fixes are written to binary restart -files. -

    -

    The fix_modify temp option is supported by these -fixes. You can use it to assign a temperature compute -you have defined to these fixes which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -these fixes and by the compute should be the same. -

    -

    These fixes can ramp its target temperature over multiple runs, using -the start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    These fixes are not invoked during energy minimization. -

    -

    These fixes compute a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to the fix. The scalar value -calculated by this fix is "extensive". -

    -

    Restrictions: -

    -

    These fixes are not compatible with fix shake. -

    -

    The fix can be used with dynamic groups as defined by the -group command. Likewise it can be used with groups to -which atoms are added or deleted over time, e.g. a deposition -simulation. However, the conservation properties of the thermostat -and barostat are defined for systems with a static set of atoms. You -may observe odd behavior if the atoms in a group vary dramatically -over time or the atom count becomes very small. -

    -

    Related commands: -

    -

    fix nve, fix nvt, fix -temp/rescale, fix langevin, -fix_modify, compute temp, -fix temp/berendsen -

    -

    Default: none -

    -
    - - - -(Bussi1) Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007) - - -

    (Bussi2) Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007) -

    - diff --git a/doc/doc2/fix_temp_rescale.html b/doc/doc2/fix_temp_rescale.html deleted file mode 100644 index 208a2de9db..0000000000 --- a/doc/doc2/fix_temp_rescale.html +++ /dev/null @@ -1,184 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix temp/rescale command -

    -

    fix temp/rescale/cuda command -

    -

    fix temp/rescale/limit/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID temp/rescale N Tstart Tstop window fraction 
-
    -
    • ID, group-ID are documented in fix command - -
    • temp/rescale = style name of this fix command - -
    • N = perform rescaling every N steps - -
    • Tstart,Tstop = desired temperature at start/end of run (temperature units) - -
        Tstart can be a variable (see below) 
-
      -
    • window = only rescale if temperature is outside this window (temperature units) - -
    • fraction = rescale to target temperature by this fraction -
    -

    Examples: -

    -
    fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 
-
    -

    Description: -

    -

    Reset the temperature of a group of atoms by explicitly rescaling -their velocities. -

    -

    The rescaling is applied to only the translational degrees of freedom -for the particles, which is an important consideration if finite-size -particles which have rotational degrees of freedom are being -thermostatted with this fix. The translational degrees of freedom can -also have a bias velocity removed from them before thermostatting -takes place; see the description below. -

    -

    Rescaling is performed every N timesteps. The target temperature is a -ramped value between the Tstart and Tstop temperatures at the -beginning and end of the run. -

    -

    Tstart can be specified as an equal-style variable. -In this case, the Tstop setting is ignored. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the target temperature. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. -

    -

    Rescaling is only performed if the difference between the current and -desired temperatures is greater than the window value. The amount -of rescaling that is applied is a fraction (from 0.0 to 1.0) of the -difference between the actual and desired temperature. E.g. if -fraction = 1.0, the temperature is reset to exactly the desired -value. -

    -

    IMPORTANT NOTE: Unlike the fix nvt command which -performs Nose/Hoover thermostatting AND time integration, this fix -does NOT perform time integration. It only modifies velocities to -effect thermostatting. Thus you must use a separate time integration -fix, like fix nve to actually update the positions of -atoms using the modified velocities. Likewise, this fix should not -normally be used on atoms that also have their temperature controlled -by another fix - e.g. by fix nvt or fix -langevin commands. -

    -

    See this howto section of the manual for -a discussion of different ways to compute temperature and perform -thermostatting. -

    -

    This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp", as if one of this command had -been issued: -

    -
    compute fix-ID_temp group-ID temp 
-
    -

    See the compute temp for details. Note that the -ID of the new compute is the fix-ID + underscore + "temp", and the -group for the new compute is the same as the fix group. -

    -

    Note that this is NOT the compute used by thermodynamic output (see -the thermo_style command) with ID = thermo_temp. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -compute_modify command or print this temperature -during thermodynamic output via the thermo_style -custom command using the appropriate compute-ID. -It also means that changing attributes of thermo_temp will have no -effect on this fix. -

    -

    Like other fixes that perform thermostatting, this fix can be used -with compute commands that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the fix_modify command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual compute -commands to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a temperature compute -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change implied by a velocity rescaling to the -system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix langevin, fix nvt, -fix_modify -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_temp_rescale_eff.html b/doc/doc2/fix_temp_rescale_eff.html deleted file mode 100644 index 038e181938..0000000000 --- a/doc/doc2/fix_temp_rescale_eff.html +++ /dev/null @@ -1,81 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix temp/rescale/eff command -

    -

    Syntax: -

    -
    fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction 
-
    -
    • ID, group-ID are documented in fix command -
    • temp/rescale/eff = style name of this fix command -
    • N = perform rescaling every N steps -
    • Tstart,Tstop = desired temperature at start/end of run (temperature units) -
    • window = only rescale if temperature is outside this window (temperature units) -
    • fraction = rescale to target temperature by this fraction -
    -

    Examples: -

    -
    fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 
-
    -

    Description: -

    -

    Reset the temperature of a group of nuclei and electrons in the -electron force field model by explicitly rescaling -their velocities. -

    -

    The operation of this fix is exactly like that described by the fix -temp/rescale command, except that the rescaling -is also applied to the radial electron velocity for electron -particles. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify temp option is supported by this -fix. You can use it to assign a temperature compute -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. -

    -

    The fix_modify energy option is supported by this -fix to add the energy change implied by a velocity rescaling to the -system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". -

    -

    This fix can ramp its target temperature over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    fix langevin/eff, fix -nvt/eff, fix_modify, -fix_temp_rescale, -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_tfmc.html b/doc/doc2/fix_tfmc.html deleted file mode 100644 index dd69b02f96..0000000000 --- a/doc/doc2/fix_tfmc.html +++ /dev/null @@ -1,168 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix tfmc command -

    -

    Syntax: -

    -
    fix ID group-ID tfmc Delta Temp seed keyword value 
-
    -
    • ID, group-ID are documented in fix command - -
    • tfmc = style name of this fix command - -
    • Delta = maximal displacement length (distance units) - -
    • Temp = imposed temperature of the system - -
    • seed = random number seed (positive integer) - -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = com or rot - -
        com args = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include each dimension
-  rot args = none 
-
      - -
    -

    Examples: -

    -
    fix 1 all tfmc 0.1 1000.0 159345
-fix 1 all tfmc 0.05 600.0 658943 com 1 1 0 
-fix 1 all tfmc 0.1 750.0 387068 com 1 1 1 rot 
-
    -

    Description: -

    -

    Perform uniform-acceptance force-bias Monte Carlo (fbMC) simulations, -using the time-stamped force-bias Monte Carlo (tfMC) algorithm -described in (Mees) and (Bal). -

    -

    One successful use case of force-bias Monte Carlo methods is that they -can be used to extend the time scale of atomistic simulations, in -particular when long time scale relaxation effects must be considered; -some interesting examples are given in the review by (Neyts). -An example of a typical use case would be the modelling of chemical -vapour deposition (CVD) processes on a surface, in which impacts by -gas-phase species can be performed using MD, but subsequent relaxation -of the surface is too slow to be done using MD only. Using tfMC can -allow for a much faster relaxation of the surface, so that higher -fluxes can be used, effectively extending the time scale of the -simulation. (Such an alternating simulation approach could be set up -using a loop.) -

    -

    The initial version of tfMC algorithm in (Mees) contained an -estimation of the effective time scale of such a simulation, but it -was later shown that the speed-up one can gain from a tfMC simulation -is system- and process-dependent, ranging from none to several orders -of magnitude. In general, solid-state processes such as -(re)crystallisation or growth can be accelerated by up to two or three -orders of magnitude, whereas diffusion in the liquid phase is not -accelerated at all. The observed pseudodynamics when using the tfMC -method is not the actual dynamics one would obtain using MD, but the -relative importance of processes can match the actual relative -dynamics of the system quite well, provided Delta is chosen with -care. Thus, the system's equilibrium is reached faster than in MD, -along a path that is generally roughly similar to a typical MD -simulation (but not necessarily so). See (Bal) for details. -

    -

    Each step, all atoms in the selected group are displaced using the -stochastic tfMC algorithm, which is designed to sample the canonical -(NVT) ensemble at the temperature Temp. Although tfMC is a Monte -Carlo algorithm and thus strictly speaking does not perform time -integration, it is similar in the sense that it uses the forces on all -atoms in order to update their positions. Therefore, it is implemented -as a time integration fix, and no other fixes of this type (such as -fix nve) should be used at the same time. Because -velocities do not play a role in this kind of Monte Carlo simulations, -instantaneous temperatures as calculated by temperature -computes or thermodynamic -output have no meaning: the only relevant -temperature is the sampling temperature Temp. Similarly, performing -tfMC simulations does not require setting a timestep -and the simulated time as calculated by LAMMPS is -meaningless. -

    -

    The critical parameter determining the success of a tfMC simulation is -Delta, the maximal displacement length of the lightest element in -the system: the larger it is, the longer the effective time scale of -the simulation will be (there is an approximately quadratic -dependence). However, Delta must also be chosen sufficiently small -in order to comply with detailed balance; in general values between 5 -and 10 % of the nearest neighbor distance are found to be a good -choice. For a more extensive discussion with specific examples, please -refer to (Bal), which also describes how the code calculates -element-specific maximal displacements from Delta, based on the -fourth root of their mass. -

    -

    Because of the uncorrelated movements of the atoms, the center-of-mass -of the fix group will not necessarily be stationary, just like its -orientation. When the com keyword is used, all atom positions will -be shifted (after every tfMC iteration) in order to fix the position -of the center-of-mass along the included directions, by setting the -corresponding flag to 1. The rot keyword does the same for the -rotational component of the tfMC displacements after every iteration. -

    -

    IMPORTANT NOTE: the com and rot keywords should not be used if an -external force is acting on the specified fix group, along the -included directions. This can be either a true external force (e.g. -through fix wall) or forces due to the interaction -with atoms not included in the fix group. This is because in such -cases, translations or rotations of the fix group could be induced by -these external forces, and removing them will lead to a violation of -detailed balance. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    None of the fix_modify options are relevant to this -fix. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    This fix is not compatible with fix shake. -

    -

    Related commands: -

    -

    fix gcmc, fix nvt -

    -

    Default: -

    -

    The option default is com = 0 0 0 -

    -
    - - - -

    (Bal) K. M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014). -

    - - -

    (Mees) M. J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and -A. Stesmans, Phys. Rev. B 85, 134301 (2012). -

    - - -

    (Neyts) E. C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 -(2013). -

    - diff --git a/doc/doc2/fix_thermal_conductivity.html b/doc/doc2/fix_thermal_conductivity.html deleted file mode 100644 index ec5fcc0407..0000000000 --- a/doc/doc2/fix_thermal_conductivity.html +++ /dev/null @@ -1,177 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix thermal/conductivity command -

    -

    Syntax: -

    -
    fix ID group-ID thermal/conductivity N edim Nbin keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • thermal/conductivity = style name of this fix command - -
    • N = perform kinetic energy exchange every N steps - -
    • edim = x or y or z = direction of kinetic energy transfer - -
    • Nbin = # of layers in edim direction (must be even number) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = swap - -
        swap value = Nswap = number of swaps to perform every N steps 
-
      - -
    -

    Examples: -

    -
    fix 1 all thermal/conductivity 100 z 20
-fix 1 all thermal/conductivity 50 z 20 swap 2 
-
    -

    Description: -

    -

    Use the Muller-Plathe algorithm described in this -paper to exchange kinetic energy between two particles -in different regions of the simulation box every N steps. This -induces a temperature gradient in the system. As described below this -enables the thermal conductivity of a material to be calculated. This -algorithm is sometimes called a reverse non-equilibrium MD (reverse -NEMD) approach to computing thermal conductivity. This is because the -usual NEMD approach is to impose a temperature gradient on the system -and measure the response as the resulting heat flux. In the -Muller-Plathe method, the heat flux is imposed, and the temperature -gradient is the system's response. -

    -

    See the compute heat/flux command for details -on how to compute thermal conductivity in an alternate way, via the -Green-Kubo formalism. -

    -

    The simulation box is divided into Nbin layers in the edim -direction, where the layer 1 is at the low end of that dimension and -the layer Nbin is at the high end. Every N steps, Nswap pairs of -atoms are chosen in the following manner. Only atoms in the fix group -are considered. The hottest Nswap atoms in layer 1 are selected. -Similarly, the coldest Nswap atoms in the "middle" layer (see below) -are selected. The two sets of Nswap atoms are paired up and their -velocities are exchanged. This effectively swaps their kinetic -energies, assuming their masses are the same. If the masses are -different, an exchange of velocities relative to center of mass motion -of the 2 atoms is performed, to conserve kinetic energy. Over time, -this induces a temperature gradient in the system which can be -measured using commands such as the following, which writes the -temperature profile (assuming z = edim) to the file tmp.profile: -

    -
    compute   ke all ke/atom
-variable  temp atom c_ke/1.5
-fix       3 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
-            file tmp.profile units reduced 
-
    -

    Note that by default, Nswap = 1, though this can be changed by the -optional swap keyword. Setting this parameter appropriately, in -conjunction with the swap rate N, allows the heat flux to be adjusted -across a wide range of values, and the kinetic energy to be exchanged -in large chunks or more smoothly. -

    -

    The "middle" layer for velocity swapping is defined as the Nbin/2 + -1 layer. Thus if Nbin = 20, the two swapping layers are 1 and 11. -This should lead to a symmetric temperature profile since the two -layers are separated by the same distance in both directions in a -periodic sense. This is why Nbin is restricted to being an even -number. -

    -

    As described below, the total kinetic energy transferred by these -swaps is computed by the fix and can be output. Dividing this -quantity by time and the cross-sectional area of the simulation box -yields a heat flux. The ratio of heat flux to the slope of the -temperature profile is proportional to the thermal conductivity of the -fluid, in appropriate units. See the Muller-Plathe -paper for details. -

    -

    IMPORTANT NOTE: If your system is periodic in the direction of the -heat flux, then the flux is going in 2 directions. This means the -effective heat flux in one direction is reduced by a factor of 2. You -will see this in the equations for thermal conductivity (kappa) in the -Muller-Plathe paper. LAMMPS is simply tallying kinetic energy which -does not account for whether or not your system is periodic; you must -use the value appropriately to yield a kappa for your system. -

    -

    IMPORTANT NOTE: After equilibration, if the temperature gradient you -observe is not linear, then you are likely swapping energy too -frequently and are not in a regime of linear response. In this case -you cannot accurately infer a thermal conductivity and should try -increasing the Nevery parameter. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative kinetic energy transferred between the bottom and middle -of the simulation box (in the edim direction) is stored as a scalar -quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the -quantity are energy; see the units command for details. -The scalar value calculated by this fix is "intensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Swaps conserve both momentum and kinetic energy, even if the masses of -the swapped atoms are not equal. Thus you should not need to -thermostat the system. If you do use a thermostat, you may want to -apply it only to the non-swapped dimensions (other than vdim). -

    -

    LAMMPS does not check, but you should not use this fix to swap the -kinetic energy of atoms that are in constrained molecules, e.g. via -fix shake or fix rigid. This is -because application of the constraints will alter the amount of -transferred momentum. You should, however, be able to use flexible -molecules. See the Zhang paper for a discussion and results -of this idea. -

    -

    When running a simulation with large, massive particles or molecules -in a background solvent, you may want to only exchange kinetic energy -bewteen solvent particles. -

    -

    Related commands: -

    -

    fix ave/spatial, fix -viscosity, compute -heat/flux -

    -

    Default: -

    -

    The option defaults are swap = 1. -

    -
    - - - -

    (Muller-Plathe) Muller-Plathe, J Chem Phys, 106, 6082 (1997). -

    - - -

    (Zhang) Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, -109, 15060-15067 (2005). -

    - diff --git a/doc/doc2/fix_ti_rs.html b/doc/doc2/fix_ti_rs.html deleted file mode 100644 index c6f60635ec..0000000000 --- a/doc/doc2/fix_ti_rs.html +++ /dev/null @@ -1,156 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ti/rs command -

    -

    Syntax: -

    -
    fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ti/rs = style name of this fix command - -
    • lambda_initial/lambda_final = initial/final values of the coupling parameter - -
    • t_switch/t_equil = number of steps of the switching/equilibration procedure - -
    • keyword = function - -
        function value = function-ID
-    function-ID = ID of the switching function (1, 2 or 3) 
-
      - -
    -

    Example: -

    -
    fix ref all ti/rs 50.0 2000 1000 
-fix vf vacancy ti/rs 10.0 70000 50000 function 2 
-
    -

    Description: -

    -

    This fix allows you to compute the free energy temperature dependence -by performing a thermodynamic integration procedure known as -Reversible Scaling (de Koning99, de -Koning00a). The thermodynamic integration is performed -using the nonequilibrium method of Adiabatic Switching -(Watanabe, de Koning96). -

    -

    The forces on the atoms are dynamically scaled during the simulation, -the rescaling is done in the following manner: -

    -
    -
    -

    where F_int is the total force on the atoms due to the interatomic -potential and lambda is the coupling parameter of the thermodynamic -integration. -

    -

    The fix acts as follows: during the first t_equil steps after the -fix is defined the value of lambda is lambda_initial , this is the -period to equilibrate the system in the lambda = lambda_initial -state. After this the value of lambda changes continuously from -lambda_initial to lambda_final according to the function defined -using the keyword function (described below), this is done in -t_switch steps. Then comes the second equilibration period of -t_equil to equilibrate the system in the lambda = lambda_final -state. After that the switching back to the lambda = lambda_initial -state is done using t_switch timesteps and following the same -switching function. After this period the value of lambda is kept -equal to lambda_initial indefinitely or until a unfix -erase the fix. -

    -

    The description of thermodynamic integration in both directions is -done in de Koning00b, the main reason is to try to -eliminate the dissipated heat due to the nonequilibrium process. -

    -

    The function keyword allows the use of three different switching -rates. The option 1 results in a constant rescaling where the lambda -parameter changes at a constant rate during the switching time -according to the switching function -

    -
    -
    -

    where tau is the scaled time variable t/t_switch. This switching -function has the characteristic that the temperature scaling is faster -at temperatures closer to the final temperature of the procedure. The -option number 2 performs the switching at a rate defined by the -following switching function -

    -
    -
    -

    This switching function has the characteristic that the temperature -scaling occurs at a constant rate during all the procedure. The option -number 3 performs the switching at a rate defined by the following -switching function -

    -
    -
    -

    This switching function has the characteristic that the temperature -scaling is faster at temperatures closer to the initial temperature of -the procedure. -

    -

    An example script using this command is provided in the -examples/USER/misc/ti directory. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    This fix computes a global vector quantitie which can be accessed by -various output commands. The vector has -2 positions, the first one is the coupling parameter lambda and the -second one is the time derivative of lambda. The scalar and vector -values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    Related commands: -

    -

    fix ti/spring -

    -

    Restrictions: -

    -

    This command is part of the USER-MISC package. It is only enabled if -LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    Default: -

    -

    The keyword default is function = 1. -

    -
    - - - -

    (de Koning 99) M. de Koning, A. Antonelli and S. Yip, Phys Rev Lett, 83, 3973 (1999). -

    - - -

    (Watanabe) M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990). -

    - - -

    (de Koning 96) M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996). -

    - - -

    (de Koning 00a) M. de Koning, A. Antonelli and S. Yip, J Chem Phys, 115, 11025 (2000). -

    - - -

    (de Koning 00b) M. de Koning et al., Computing in Science & Engineering, 2, 88 (2000). -

    - diff --git a/doc/doc2/fix_ti_spring.html b/doc/doc2/fix_ti_spring.html deleted file mode 100644 index 7aa8255b43..0000000000 --- a/doc/doc2/fix_ti_spring.html +++ /dev/null @@ -1,175 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ti/spring command -

    -

    Syntax: -

    -
    fix ID group-ID ti/spring K t_switch t_equil keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • ti/spring = style name of this fix command - -
    • K = spring constant (force/distance units) - -
    • t_switch/t_equil = number of steps of the switching/equilibration procedure - -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = function - -
        function value = function-ID 
-    function-ID = ID of the switching function (1 or 2) 
-
      - -
    -

    Example: -

    -
    fix ref all ti/spring 50.0 2000 1000 function 2 
-
    -

    Description: -

    -

    This fix allows you to compute the free energy of solids by performing -a thermodynamic integration between the solid of interest and an -Einstein crystal (Frenkel). The thermodynamic integration -is performed using the nonequilibrium method of Adiabatic Switching -(Watanabe, de Koning96). -

    -

    A spring force is applied independently to each atom in the group to -tether it to its initial position. The initial position for each atom -is its location at the time the fix command was issued. More details -about the springs are available in fix -spring/self. The forces on the atoms are -dynamically scaled during the simulation, the rescaling is done in the -following manner: -

    -
    -
    -

    where F_harm is the force due to the springs, F_solid is the total -force on the atoms due to the interatomic potential and lambda is the -coupling parameter of the thermodynamic integration. -

    -

    The fix acts as follows: during the first t_equil steps after the -fix is defined the value of lambda is zero, this is the period to -equilibrate the system in the lambda = 0 state. After this the value -of lambda changes continuously from 0 to 1 according to the function -defined using the keyword function (described below), this is done -in t_switch steps. Then comes the second equilibration period of -t_equil to equilibrate the system in the lambda = 1 state. After -that the switching back to the lambda = 0 state is made using -t_switch timesteps and following the same switching function. After -this period the value of lambda is kept equal to zero and the fix has -no action in the dynamics of the system anymore. -

    -

    The description of thermodynamic integration in both directions is -done in de Koning97, the main reason is to try to -eliminate the dissipated heat due to the nonequilibrium process. -

    -

    The function keyword allows the use of two different switching -rates, the option 1 results in a constant rescaling where the lambda -parameter changes at a constant rate during the switching time -according to the switching function -

    -
    -
    -

    where tau is the scaled time variable t/t_switch. The option number -2 performs the switching at a rate defined by the following -switching function -

    -
    -
    -

    This function has zero slope as lambda approaches its extreme values -(0 and 1), according to (de Koning96) this results in -smaller fluctuations on the integral to be computed on the -thermodynamic integration. -

    -

    IMPORTANT NOTE: It is importante to keep the center of mass fixed -during the thermodynamic integration, a non-zero total velocity will -result in divergencies during the integration due to the fact that the -atoms are 'attatched' to its equilibrium positions by the Einstein -crystal. Check the option zero of fix langevin -and velocity. The use of the Nose-Hoover thermostat -(fix nvt) is NOT recommended due to its well documented -issues with the canonical sampling of harmonic degrees of freedom -(notice that the chain option will NOT solve this problem). The -Langevin thermostat (fix langevin) works fine. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the original coordinates of tethered atoms to binary -restart files, so that the spring effect will be the -same in a restarted simulation. See the read -restart command for info on how to re-specify a fix -in an input script that reads a restart file, so that the operation of -the fix continues in an uninterrupted fashion. -

    -

    The fix modify energy option is supported by this -fix to add the energy stored in the per-atom springs to the system's -potential energy as part of thermodynamic output. -

    -

    This fix computes a global scalar and a global vector quantities which -can be accessed by various output -commands. The scalar is an energy which -is the sum of the spring energy for each atom, where the per-atom -energy is 0.5 * K * r^2. The vector has 2 positions, the first one is -the coupling parameter lambda and the second one is the time -derivative of lambda. The scalar and vector values calculated by this -fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    IMPORTANT NOTE: If you want the per-atom spring energy to be included -in the total potential energy of the system (the quantity being -minimized), you MUST enable the fix modify energy -option for this fix. -

    -

    An example script using this command is provided in the -examples/USER/misc/ti directory. -

    -

    Related commands: -

    -

    fix spring, fix ti/rs -

    -

    Restrictions: -

    -

    This command is part of the USER-MISC package. It is only enabled if -LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    Default: -

    -

    The keyword default is function = 1. -

    -
    - - - -

    (Frenkel) Daan Frenkel and Anthony J. C. Ladd, J. Chem. Phys. 81, 3188 -(1984). -

    - - -

    (Watanabe) M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990). -

    - - -

    (de Koning 96) M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996). -

    - - -

    (de Koning 97) M. de Koning and A. Antonelli, Phys Rev B, 55, 735 (1997). -

    - diff --git a/doc/doc2/fix_tmd.html b/doc/doc2/fix_tmd.html deleted file mode 100644 index c365365f4b..0000000000 --- a/doc/doc2/fix_tmd.html +++ /dev/null @@ -1,138 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix tmd command -

    -

    Syntax: -

    -
    fix ID group-ID tmd rho_final file1 N file2 
-
    -
    • ID, group-ID are documented in fix command -
    • tmd = style name of this fix command -
    • rho_final = desired value of rho at the end of the run (distance units) -
    • file1 = filename to read target structure from -
    • N = dump TMD statistics every this many timesteps, 0 = no dump -
    • file2 = filename to write TMD statistics to (only needed if N > 0) -
    -

    Examples: -

    -
    fix 1 all nve
-fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file 
-
    -

    Description: -

    -

    Perform targeted molecular dynamics (TMD) on a group of atoms. A -holonomic constraint is used to force the atoms to move towards (or -away from) the target configuration. The parameter "rho" is -monotonically decreased (or increased) from its initial value to -rho_final at the end of the run. -

    -

    Rho has distance units and is a measure of the root-mean-squared -distance (RMSD) between the current configuration of the atoms in the -group and the target coordinates listed in file1. Thus a value of -rho_final = 0.0 means move the atoms all the way to the final -structure during the course of the run. -

    -

    The target file1 can be ASCII text or a gzipped text file (detected by -a .gz suffix). The format of the target file1 is as follows: -

    -
    0.0 25.0 xlo xhi
-0.0 25.0 ylo yhi
-0.0 25.0 zlo zhi
-125     24.97311   1.69005     23.46956 0 0 -1
-126     1.94691    2.79640     1.92799  1 0 0
-127     0.15906    3.46099     0.79121  1 0 0
-... 
-
    -

    The first 3 lines may or may not be needed, depending on the format of -the atoms to follow. If image flags are included with the atoms, the -1st 3 lo/hi lines must appear in the file. If image flags are not -included, the 1st 3 lines should not appear. The 3 lines contain the -simulation box dimensions for the atom coordinates, in the same format -as in a LAMMPS data file (see the read_data command). -

    -

    The remaining lines each contain an atom ID and its target x,y,z -coordinates. The atom lines (all or none of them) can optionally be -followed by 3 integer values: nx,ny,nz. For periodic dimensions, they -specify which image of the box the atom is considered to be in, i.e. a -value of N (positive or negative) means add N times the box length to -the coordinate to get the true value. -

    -

    The atom lines can be listed in any order, but every atom in the group -must be listed in the file. Atoms not in the fix group may also be -listed; they will be ignored. -

    -

    TMD statistics are written to file2 every N timesteps, unless N is -specified as 0, which means no statistics. -

    -

    The atoms in the fix tmd group should be integrated (via a fix nve, -nvt, npt) along with other atoms in the system. -

    -

    Restarts can be used with a fix tmd command. For example, imagine a -10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a -restart file was written after 2000 time steps, then the configuration -in the file would have a rho value of 9. A new 8000 time step run -could be performed with the same rho_final = 1 to complete the -conformational change at the same transition rate. Note that for -restarted runs, the name of the TMD statistics file should be changed -to prevent it being overwritten. -

    -

    For more information about TMD, see (Schlitter1) and -(Schlitter2). -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. -

    -

    This fix can ramp its rho parameter over multiple runs, using the -start and stop keywords of the run command. See the -run command for details of how to do this. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    All TMD fixes must be listed in the input script after all integrator -fixes (nve, nvt, npt) are applied. This ensures that atoms are moved -before their positions are corrected to comply with the constraint. -

    -

    Atoms that have a TMD fix applied should not be part of a group to -which a SHAKE fix is applied. This is because LAMMPS assumes there -are not multiple competing holonomic constraints applied to the same -atoms. -

    -

    To read gzipped target files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the Making -LAMMPS section of the documentation. -

    -

    Related commands: none -

    -

    Default: none -

    -
    - - - -

    (Schlitter1) Schlitter, Swegat, Mulders, "Distance-type reaction -coordinates for modelling activated processes", J Molecular Modeling, -7, 171-177 (2001). -

    - - -

    (Schlitter2) Schlitter and Klahn, "The free energy of a reaction -coordinate at multiple constraints: a concise formulation", Molecular -Physics, 101, 3439-3443 (2003). -

    - diff --git a/doc/doc2/fix_ttm.html b/doc/doc2/fix_ttm.html deleted file mode 100644 index ff7a396989..0000000000 --- a/doc/doc2/fix_ttm.html +++ /dev/null @@ -1,350 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix ttm command -

    -

    fix ttm/mod command -

    -

    Syntax: -

    -
    fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
-fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile 
-
    -
    • ID, group-ID are documented in fix command - -
    • style = ttm or ttm_mod - -
    • seed = random number seed to use for white noise (positive integer) - -
    • remaining arguments for fix ttm: - -
        C_e  = electronic specific heat (energy/(electron*temperature) units)
-  rho_e = electronic density (electrons/volume units)
-  kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
-  gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
-  gamma_s = friction coefficient due to electronic stopping (mass/time units)
-  v_0 = electronic stopping critical velocity (velocity units)
-  Nx = number of thermal solve grid points in the x-direction (positive integer)
-  Ny = number of thermal solve grid points in the y-direction (positive integer)
-  Nz = number of thermal solve grid points in the z-direction (positive integer)
-  T_infile = filename to read initial electronic temperature from
-  N = dump TTM temperatures every this many timesteps, 0 = no dump
-  T_outfile = filename to write TTM temperatures to (only needed if N > 0) 
-
      -
    • remaining arguments for fix ttm/mod: - -
        init_file = file with the parameters to TTM
-  Nx = number of thermal solve grid points in the x-direction (positive integer)
-  Ny = number of thermal solve grid points in the y-direction (positive integer)
-  Nz = number of thermal solve grid points in the z-direction (positive integer)
-  T_infile = filename to read initial electronic temperature from
-  N = dump TTM temperatures every this many timesteps, 0 = no dump
-  T_outfile = filename to write TTM temperatures to (only needed if N > 0) 
-
      - -
    -

    Examples: -

    -
    fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
-fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
-fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out 
-
    -

    Description: -

    -

    Use a two-temperature model (TTM) to represent heat transfer through -and between electronic and atomic subsystems. LAMMPS models the -atomic subsystem as usual with a molecular dynamics model and the -classical force field specified by the user, but the electronic -subsystem is modeled as a continuum, or a background "gas", on a -regular grid. Energy can be transferred spatially within the grid -representing the electrons. Energy can also be transferred between -the electronic and the atomic subsystems. The algorithm underlying -this fix was derived by D. M. Duffy and A. M. Rutherford and is -discussed in two J Physics: Condensed Matter papers: (Duffy) -and (Rutherford). They used this algorithm in cascade -simulations where a primary knock-on atom (PKA) was initialized with a -high velocity to simulate a radiation event. -

    -

    The description in this sub-section applies to both fix ttm and fix -ttm/mod. Fix ttm/mod adds options to account for external heat -sources (e.g. at a surface) and for specifying parameters that allow -the electronic heat capacity to depend strongly on electronic -temperature. It is more expensive computationally than fix ttm -because it treats the thermal diffusion equation as non-linear. More -details on fix ttm/mod are given below. -

    -

    Heat transfer between the electronic and atomic subsystems is carried -out via an inhomogeneous Langevin thermostat. This thermostat differs -from the regular Langevin thermostat (fix -langevin) in three important ways. First, the -Langevin thermostat is applied uniformly to all atoms in the -user-specified group for a single target temperature, whereas the TTM -fix applies Langevin thermostatting locally to atoms within the -volumes represented by the user-specified grid points with a target -temperature specific to that grid point. Second, the Langevin -thermostat couples the temperature of the atoms to an infinite heat -reservoir, whereas the heat reservoir for fix TTM is finite and -represents the local electrons. Third, the TTM fix allows users to -specify not just one friction coefficient, but rather two independent -friction coefficients: one for the electron-ion interactions -(gamma_p), and one for electron stopping (gamma_s). -

    -

    When the friction coefficient due to electron stopping, gamma_s, is -non-zero, electron stopping effects are included for atoms moving -faster than the electron stopping critical velocity, v_0. For -further details about this algorithm, see (Duffy) and -(Rutherford). -

    -

    Energy transport within the electronic subsystem is solved according -to the heat diffusion equation with added source terms for heat -transfer between the subsystems: -

    -
    -
    -

    where C_e is the specific heat, rho_e is the density, kappa_e is the -thermal conductivity, T is temperature, the "e" and "a" subscripts -represent electronic and atomic subsystems respectively, g_p is the -coupling constant for the electron-ion interaction, and g_s is the -electron stopping coupling parameter. C_e, rho_e, and kappa_e are -specified as parameters to the fix. The other quantities are derived. -The form of the heat diffusion equation used here is almost the same -as that in equation 6 of (Duffy), with the exception that the -electronic density is explicitly reprensented, rather than being part -of the the specific heat parameter. -

    -

    Currently, fix ttm assumes that none of the user-supplied parameters -will vary with temperature. Note that (Duffy) used a tanh() -functional form for the temperature dependence of the electronic -specific heat, but ignored temperature dependencies of any of the -other parameters. See more discussion below for fix ttm/mod. -

    -

    These fixes require use of periodic boundary conditions and a 3D -simulation. Periodic boundary conditions are also used in the heat -equation solve for the electronic subsystem. This varies from the -approach of (Rutherford) where the atomic subsystem was -embedded within a larger continuum representation of the electronic -subsystem. -

    -

    The initial electronic temperature input file, T_infile, is a text -file LAMMPS reads in with no header and with four numeric columns -(ix,iy,iz,Temp) and with a number of rows equal to the number of -user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are node -indices from 0 to nxnodes-1, etc. For example, the initial electronic -temperatures on a 1 by 2 by 3 grid could be specified in a T_infile -as follows: -

    -
    0 0 0 1.0
-0 0 1 1.0
-0 0 2 1.0
-0 1 0 2.0
-0 1 1 2.0
-0 1 2 2.0 
-
    -

    where the electronic temperatures along the y=0 plane have been set to -1.0, and the electronic temperatures along the y=1 plane have been set -to 2.0. The order of lines in this file is no important. If all the -nodal values are not specified, LAMMPS will generate an error. -

    -

    The temperature output file, T_oufile, is created and written by -this fix. Temperatures for both the electronic and atomic subsystems -at every node and every N timesteps are output. If N is specified as -zero, no output is generated, and no output filename is needed. The -format of the output is as follows. One long line is written every -output timestep. The timestep itself is given in the first column. -The next Nx*Ny*Nz columns contain the temperatures for the atomic -subsystem, and the final Nx*Ny*Nz columns contain the temperatures for -the electronic subsystem. The ordering of the Nx*Ny*Nz columns is -with the z index varing fastest, y the next fastest, and x the -slowest. -

    -

    These fixes do not change the coordinates of their atoms; they only -scales their velocities. Thus a time integration fix (e.g. fix -nve) should still be used to time integrate the affected -atoms. The fixes should not normally be used on atoms that have their -temperature controlled by another fix - e.g. fix nvt or -fix langevin. -

    -

    IMPORTANT NOTE: The current implementations of these fixes create a -copy of the electron grid that overlays the entire simulation domain, -for each processor. Values on the grid are summed across all -processors. Thus you should insure that this grid is not too large, -else your simulation could incur high memory and communication costs. -

    -
    - -

    Additional details for fix ttm/mod -

    -

    Fix ttm/mod uses the heat diffusion equation with possible external -heat sources (e.g. laser heating in ablation simulations): -

    -
    -
    -

    where theta is the Heaviside step function, I_0 is the (absorbed) -laser pulse intensity for ablation simulations, l_skin is the depth -of skin-layer, and all other designations have the same meaning as in -the former equation. The duration of the pulse is set by the parameter -tau in the init_file. -

    -

    Fix ttm/mod also allows users to specify the dependencies of C_e and -kappa_e on the electronic temperature. The specific heat is expressed -as -

    -
    -
    -

    where X = T_e/1000, and the thermal conductivity is defined as -kappa_e = D_e*rho_e*C_e, where D_e is the thermal diffusion -coefficient. -

    -

    Electronic pressure effects are included in the TTM model to account -for the blast force acting on ions because of electronic pressure -gradient (see (Chen), (Norman)). The total force -acting on an ion is: -

    -
    -
    -

    where F_langevin is a force from Langevin thermostat simulating -electron-phonon coupling, and nabla P_e/n_ion is the electron blast -force. -

    -

    The electronic pressure is taken to be P_e = B*rho_e*C_e*T_e -

    -

    The current fix ttm/mod implementation allows TTM simulations with a -vacuum. The vacuum region is defined as the grid cells with zero -electronic temperature. The numerical scheme does not allow energy -exchange with such cells. Since the material can expand to previously -unoccupied region in some simulations, the vacuum border can be -allowed to move. It is controlled by the surface_movement parameter -in the init_file. If it is set to 1, then "vacuum" cells can be -changed to "electron-filled" cells with the temperature T_e_min if -atoms move into them (currently only implemented for the case of -1-dimensional motion of flat surface normal to the X axis). The -initial borders of vacuum can be set in the init_file via lsurface -and rsurface parameters. In this case, electronic pressure gradient -is calculated as -

    -
    -
    -

    where lambda is the electron mean free path (see (Norman), -(Pisarev)) -

    -

    The fix ttm/mod parameter file init_file has the following syntax/ -Every line with the odd number is considered as a comment and -ignored. The lines with the even numbers are treated as follows: -

    -
    a_0, energy/(temperature*electron) units
-a_1, energy/(temperature^2*electron) units
-a_2, energy/(temperature^3*electron) units
-a_3, energy/(temperature^4*electron) units
-a_4, energy/(temperature^5*electron) units
-C_0, energy/(temperature*electron) units
-A, 1/temperature units
-rho_e, electrons/volume units
-D_e, length^2/time units
-gamma_p, mass/time units
-gamma_s, mass/time units
-v_0, length/time units
-I_0, energy/(time*length^2) units
-lsurface, electron grid units (positive integer)
-rsurface, electron grid units (positive integer)
-l_skin, length units
-tau, time units
-B, dimensionless
-lambda, length units
-n_ion, ions/volume units
-surface_movement: 0 to disable tracking of surface motion, 1 to enable
-T_e_min, temperature units 
-
    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    These fixes write the state of the electronic subsystem and the energy -exchange between the subsystems to binary restart -files. See the read_restart command -for info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    Because the state of the random number generator is not saved in the -restart files, this means you cannot do "exact" restarts with this -fix, where the simulation continues on the same as if no restart had -taken place. However, in a statistical sense, a restarted simulation -should produce the same behavior. -

    -

    None of the fix_modify options are relevant to these -fixes. -

    -

    Both fixes compute 2 output quantities stored in a vector of length 2, -which can be accessed by various output -commands. The first quantity is the -total energy of the electronic subsystem. The second quantity is the -energy transferred from the electronic to the atomic subsystem on that -timestep. Note that the velocity verlet integrator applies the fix ttm -forces to the atomic subsystem as two half-step velocity updates: one -on the current timestep and one on the subsequent timestep. -Consequently, the change in the atomic subsystem energy is lagged by -half a timestep relative to the change in the electronic subsystem -energy. As a result of this, users may notice slight fluctuations in -the sum of the atomic and electronic subsystem energies reported at -the end of the timestep. -

    -

    The vector values calculated are "extensive". -

    -

    No parameter of the fixes can be used with the start/stop keywords -of the run command. The fixes are not invoked during -energy minimization. -

    -

    Restrictions: -

    -

    Fix ttm is part of the MISC package. It is only enabled if LAMMPS -was built with that package. Fix ttm/mod is part of the USER-MISC -package. It is only enabled if LAMMPS was built with that package. -See the Making LAMMPS section for more -info. -

    -

    These fixes can only be used for 3d simulations and orthogonal -simlulation boxes. You must also use periodic -boundary conditions. -

    -

    Related commands: -

    -

    fix langevin, fix dt/reset -

    -

    Default: none -

    -
    - - - -

    (Duffy) D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, -016207-016218 (2007). -

    - - -

    (Rutherford) A M Rutherford and D M Duffy, J. Phys.: -Condens. Matter, 19, 496201-496210 (2007). -

    - - -

    (Chen) J Chen, D Tzou and J Beraun, Int. J. Heat -Mass Transfer, 49, 307-316 (2006). -

    - - -

    (Norman) G E Norman, S V Starikov, V V Stegailov et al., Contrib. -Plasma Phys., 53, 129-139 (2013). -

    - - -

    (Pisarev) V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, -475401 (2014). -

    - diff --git a/doc/doc2/fix_tune_kspace.html b/doc/doc2/fix_tune_kspace.html deleted file mode 100644 index 2b21e12afd..0000000000 --- a/doc/doc2/fix_tune_kspace.html +++ /dev/null @@ -1,109 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix tune/kspace command -

    -

    Syntax: -

    -
    fix ID group-ID tune/kspace N 
-
    -
    • ID, group-ID are documented in fix command - -
    • tune/kspace = style name of this fix command - -
    • N = invoke this fix every N steps - - -
    -

    Examples: -

    -
    fix 2 all tune/kspace 100 
-
    -

    Description: -

    -

    This fix tests each kspace style (Ewald, PPPM, and MSM), and -automatically selects the fastest style to use for the remainder -of the run. If the fastest style is Ewald or PPPM, the fix also -adjusts the coulomb cutoff towards optimal speed. Future versions -of this fix will automatically select other kspace parameters -to use for maximum simulation speed. The kspace parameters may -include the style, cutoff, grid points in each direction, order, -Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc. -

    -

    The rationale for this fix is to provide the user with -as-fast-as-possible simulations that include long-range electrostatics -(kspace) while meeting the user-prescribed accuracy requirement. A -simple heuristic could never capture the optimal combination of -parameters for every possible run-time scenario. But by performing -short tests of various kspace parameter sets, this fix allows -parameters to be tailored specifically to the user's machine, MPI -ranks, use of threading or accelerators, the simulated system, and the -simulation details. In addition, it is possible that parameters could -be evolved with the simulation on-the-fly, which is useful for systems -that are dynamically evolving (e.g. changes in box size/shape or -number of particles). -

    -

    When this fix is invoked, LAMMPS will perform short timed tests of -various parameter sets to determine the optimal parameters. Tests are -performed on-the-fly, with a new test initialized every N steps. N should -be chosen large enough so that adequate CPU time lapses between tests, -thereby providing statistically significant timings. But N should not be -chosen to be so large that an unfortunate parameter set test takes an -inordinate amount of wall time to complete. An N of 100 for most problems -seems reasonable. Once an optimal parameter set is found, that set is -used for the remainder of the run. -

    -

    This fix uses heristics to guide it's selection of parameter sets to test, -but the actual timed results will be used to decide which set to use in the -simulation. -

    -

    It is not necessary to discard trajectories produced using sub-optimal -parameter sets, or a mix of various parameter sets, since the user-prescribed -accuracy will have been maintained throughout. However, some users may prefer -to use this fix only to discover the optimal parameter set for a given setup -that can then be used on subsequent production runs. -

    -

    This fix starts with kspace parameters that are set by the user with the -kspace_style and kspace_modify -commands. The prescribed accuracy will be maintained by this fix throughout -the simulation. -

    -

    None of the fix_modify options are relevant to this -fix. -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the KSPACE package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

    -

    Do not set "neigh_modify once yes" or else this fix will never be -called. Reneighboring is required. -

    -

    Related commands: -

    -

    kspace_style, boundary -kspace_modify, pair_style -lj/cut/coul/long, pair_style -lj/charmm/coul/long, pair_style -lj/long, pair_style -lj/long/coul/long, -pair_style buck/coul/long -

    -

    Default: -

    -
    - - diff --git a/doc/doc2/fix_vector.html b/doc/doc2/fix_vector.html deleted file mode 100644 index a5589ecdfc..0000000000 --- a/doc/doc2/fix_vector.html +++ /dev/null @@ -1,171 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix vector command -

    -

    Syntax: -

    -
    fix ID group-ID vector Nevery value1 value2 ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • vector = style name of this fix command - -
    • Nevery = use input values every this many timesteps - -
    • one or more input values can be listed - -
    • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name - -
        c_ID = global scalar calculated by a compute with ID
-  c_ID[I] = Ith component of global vector calculated by a compute with ID
-  f_ID = global scalar calculated by a fix with ID
-  f_ID[I] = Ith component of global vector calculated by a fix with ID
-  v_name = global value calculated by an equal-style variable with name 
-
      - -
    -

    Examples: -

    -
    fix 1 all vector 100 c_myTemp
-fix 1 all vector 5 c_myTemp v_integral 
-
    -

    Description: -

    -

    Use one or more global values as inputs every few timesteps, and -simply store them. For a single specified value, the values are -stored as a global vector of growing length. For multiple specified -values, they are stored as rows in a global array, whose number of -rows is growing. The resulting vector or array can be used by other -output commands. -

    -

    One way to to use this command is to accumulate a vector that is -time-integrated using the variable trap() function. -For example the velocity auto-correlation function (VACF) can be -time-integrated, to yield a diffusion coefficient, as follows: -

    -
    compute         2 all vacf
-fix             5 all vector 1 c_2[4]
-variable        diff equal dt*trap(f_5)
-thermo_style    custom step v_diff 
-
    -

    The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. -

    -

    Each listed value can be the result of a compute or -fix or the evaluation of an equal-style -variable. In each case, the compute, fix, or variable -must produce a global quantity, not a per-atom or local quantity. -And the global quantity must be a scalar, not a vector or array. -

    -

    Computes that produce global quantities are those which -do not have the word atom in their style name. Only a few -fixes produce global quantities. See the doc pages for -individual fixes for info on which ones produce such values. -Variables of style equal are the only ones that can -be used with this fix. Variables of style atom cannot be used, -since they produce per-atom values. -

    -

    The Nevery argument specifies on what timesteps the input values -will be used in order to be stored. Only timesteps that are a -multiple of Nevery, including timestep 0, will contribute values. -

    -

    Note that if you perform multiple runs, using the "pre no" option of -the run command to avoid initialization on subsequent runs, -then you need to use the stop keyword with the first run -command with a timestep value that encompasses all the runs. This is -so that the vector or array stored by this fix can be allocated to a -sufficient size. -

    -
    - -

    If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the compute is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the compute is used. -

    -

    Note that there is a compute reduce command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix vector. Or it can be a compute defined -not in your input script, but by thermodynamic -output or other fixes such as fix nvt -or fix temp/rescale. See the doc pages for -these commands which give the IDs of these computes. Users can also -write code for their own compute styles and add them to -LAMMPS. -

    -

    If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the fix is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the fix is used. -

    -

    Note that some fixes only produce their values on certain timesteps, -which must be compatible with Nevery, else an error will result. -Users can also write code for their own fix styles and add them to -LAMMPS. -

    -

    If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Only equal-style -variables can be referenced. See the variable command -for details. Note that variables of style equal define a formula -which can reference individual atom properties or thermodynamic -keywords, or they can invoke other computes, fixes, or variables when -they are evaluated, so this is a very general means of specifying -quantities to be stored by fix vector. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix produces a global vector or global array which can be -accessed by various output commands. -The values can only be accessed on timesteps that are multiples of -Nevery. -

    -

    A vector is produced if only a single input value is specified. -An array is produced if multiple input values are specified. -The length of the vector or the number of rows in the array grows -by 1 every Nevery timesteps. -

    -

    If the fix prouduces a vector, then the entire vector will be either -"intensive" or "extensive", depending on whether the values stored in -the vector are "intensive" or "extensive". If the fix produces an -array, then all elements in the array must be the same, either -"intensive" or "extensive". If a compute or fix provides the value -stored, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for -further info. Values produced by a variable are treated as intensive. -

    -

    This fix can allocate storage for stored values accumulated over -multiple runs, using the start and stop keywords of the -run command. See the run command for details of -how to do this. If using the run pre no command option, -this is required to allow the fix to allocate sufficient storage for -stored values. -

    -

    This fix is not invoked during energy minimization. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute, variable -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_viscosity.html b/doc/doc2/fix_viscosity.html deleted file mode 100644 index eb96df8cb7..0000000000 --- a/doc/doc2/fix_viscosity.html +++ /dev/null @@ -1,184 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix viscosity command -

    -

    Syntax: -

    -
    fix ID group-ID viscosity N vdim pdim Nbin keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • viscosity = style name of this fix command - -
    • N = perform momentum exchange every N steps - -
    • vdim = x or y or z = which momentum component to exchange - -
    • pdim = x or y or z = direction of momentum transfer - -
    • Nbin = # of layers in pdim direction (must be even number) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = swap or target - -
        swap value = Nswap = number of swaps to perform every N steps
-  vtarget value = V or INF = target velocity of swap partners (velocity units) 
-
      - -
    -

    Examples: -

    -
    fix 1 all viscosity 100 x z 20
-fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5 
-
    -

    Description: -

    -

    Use the Muller-Plathe algorithm described in this -paper to exchange momenta between two particles in -different regions of the simulation box every N steps. This induces a -shear velocity profile in the system. As described below this enables -a viscosity of the fluid to be calculated. This algorithm is -sometimes called a reverse non-equilibrium MD (reverse NEMD) approach -to computing viscosity. This is because the usual NEMD approach is to -impose a shear velocity profile on the system and measure the response -via an off-diagonal component of the stress tensor, which is -proportional to the momentum flux. In the Muller-Plathe method, the -momentum flux is imposed, and the shear velocity profile is the -system's response. -

    -

    The simulation box is divided into Nbin layers in the pdim -direction, where the layer 1 is at the low end of that dimension and -the layer Nbin is at the high end. Every N steps, Nswap pairs of -atoms are chosen in the following manner. Only atoms in the fix group -are considered. Nswap atoms in layer 1 with positive velocity -components in the vdim direction closest to the target value V are -selected. Similarly, Nswap atoms in the "middle" layer (see below) with -negative velocity components in the vdim direction closest to the -negative of the target value V are selected. The two sets of Nswap -atoms are paired up and their vdim momenta components are swapped -within each pair. This resets their velocities, typically in opposite -directions. Over time, this induces a shear velocity profile in the -system which can be measured using commands such as the following, -which writes the profile to the file tmp.profile: -

    -
    fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
-    file tmp.profile units reduced 
-
    -

    Note that by default, Nswap = 1 and vtarget = INF, though this can be -changed by the optional swap and vtarget keywords. When vtarget = -INF, one or more atoms with the most positive and negative velocity -components are selected. Setting these parameters appropriately, in -conjunction with the swap rate N, allows the momentum flux rate to be -adjusted across a wide range of values, and the momenta to be -exchanged in large chunks or more smoothly. -

    -

    The "middle" layer for momenta swapping is defined as the Nbin/2 + 1 -layer. Thus if Nbin = 20, the two swapping layers are 1 and 11. -This should lead to a symmetric velocity profile since the two layers -are separated by the same distance in both directions in a periodic -sense. This is why Nbin is restricted to being an even number. -

    -

    As described below, the total momentum transferred by these velocity -swaps is computed by the fix and can be output. Dividing this -quantity by time and the cross-sectional area of the simulation box -yields a momentum flux. The ratio of momentum flux to the slope of -the shear velocity profile is proportional to the viscosity of the -fluid, in appropriate units. See the Muller-Plathe -paper for details. -

    -

    IMPORTANT NOTE: If your system is periodic in the direction of the -momentum flux, then the flux is going in 2 directions. This means the -effective momentum flux in one direction is reduced by a factor of 2. -You will see this in the equations for viscosity in the Muller-Plathe -paper. LAMMPS is simply tallying momentum which does not account for -whether or not your system is periodic; you must use the value -appropriately to yield a viscosity for your system. -

    -

    IMPORTANT NOTE: After equilibration, if the velocity profile you -observe is not linear, then you are likely swapping momentum too -frequently and are not in a regime of linear response. In this case -you cannot accurately infer a viscosity and should try increasing -the Nevery parameter. -

    -

    An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in Section_howto -13 of the manual. NEMD simulations -deform the simmulation box via the fix deform -command. Thus they cannot be run on a charged system using a PPPM -solver since PPPM does not currently support -non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; -thus it does not suffer from this limitation. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global scalar which can be accessed by various -output commands. The scalar is the -cummulative momentum transferred between the bottom and middle of the -simulation box (in the pdim direction) is stored as a scalar -quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the -quantity are momentum = mass*velocity. The scalar value calculated by -this fix is "intensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Swaps conserve both momentum and kinetic energy, even if the masses of -the swapped atoms are not equal. Thus you should not need to -thermostat the system. If you do use a thermostat, you may want to -apply it only to the non-swapped dimensions (other than vdim). -

    -

    LAMMPS does not check, but you should not use this fix to swap -velocities of atoms that are in constrained molecules, e.g. via fix -shake or fix rigid. This is because -application of the constraints will alter the amount of transferred -momentum. You should, however, be able to use flexible molecules. -See the Maginn paper for an example of using this algorithm -in a computation of alcohol molecule properties. -

    -

    When running a simulation with large, massive particles or molecules -in a background solvent, you may want to only exchange momenta bewteen -solvent particles. -

    -

    Related commands: -

    -

    fix ave/spatial, fix -thermal/conductivity -

    -

    Default: -

    -

    The option defaults are swap = 1 and vtarget = INF. -

    -
    - - - -

    (Muller-Plathe) Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999). -

    - - -

    (Maginn) Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, -260, 218-231 (2007). -

    - diff --git a/doc/doc2/fix_viscous.html b/doc/doc2/fix_viscous.html deleted file mode 100644 index 9d890a071a..0000000000 --- a/doc/doc2/fix_viscous.html +++ /dev/null @@ -1,134 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix viscous command -

    -

    fix viscous/cuda command -

    -

    Syntax: -

    -
    fix ID group-ID viscous gamma keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • viscous = style name of this fix command - -
    • gamma = damping coefficient (force/velocity units) - -
    • zero or more keyword/value pairs may be appended - -
      keyword = scale
-  scale values = type ratio
-    type = atom type (1-N)
-    ratio = factor to scale the damping coefficient by 
-
      - -
    -

    Examples: -

    -
    fix 1 flow viscous 0.1
-fix 1 damp viscous 0.5 scale 3 2.5 
-
    -

    Description: -

    -

    Add a viscous damping force to atoms in the group that is proportional -to the velocity of the atom. The added force can be thought of as a -frictional interaction with implicit solvent, i.e. the no-slip Stokes -drag on a spherical particle. In granular simulations this can be -useful for draining the kinetic energy from the system in a controlled -fashion. If used without additional thermostatting (to add kinetic -energy to the system), it has the effect of slowly (or rapidly) -freezing the system; hence it can also be used as a simple energy -minimization technique. -

    -

    The damping force F is given by F = - gamma * velocity. The larger -the coefficient, the faster the kinetic energy is reduced. If the -optional keyword scale is used, gamma can scaled up or down by the -specified factor for atoms of that type. It can be used multiple -times to adjust gamma for several atom types. -

    -

    IMPORTANT NOTE: You should specify gamma in force/velocity units. -This is not the same as mass/time units, at least for some of the -LAMMPS units options like "real" or "metal" that are not -self-consistent. -

    -

    In a Brownian dynamics context, gamma = Kb T / D, where Kb = -Boltzmann's constant, T = temperature, and D = particle diffusion -coefficient. D can be written as Kb T / (3 pi eta d), where eta = -dynamic viscosity of the frictional fluid and d = diameter of -particle. This means gamma = 3 pi eta d, and thus is proportional to -the viscosity of the fluid and the particle diameter. -

    -

    In the current implementation, rather than have the user specify a -viscosity, gamma is specified directly in force/velocity units. If -needed, gamma can be adjusted for atoms of different sizes -(i.e. sigma) by using the scale keyword. -

    -

    Note that Brownian dynamics models also typically include a randomized -force term to thermostat the system at a chosen temperature. The fix -langevin command does this. It has the same -viscous damping term as fix viscous and adds a random force to each -atom. The random force term is proportional to the sqrt of the chosen -thermostatting temperature. Thus if you use fix langevin with a -target T = 0, its random force term is zero, and you are essentially -performing the same operation as fix viscous. Also note that the -gamma of fix viscous is related to the damping parameter of fix -langevin, however the former is specified in units -of force/velocity and the latter in units of time, so that it can more -easily be used as a thermostat. -

    -
    - -

    Styles with a cuda suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. This fix should only -be used with damped dynamics minimizers that allow for -non-conservative forces. See the min_style command -for details. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix langevin -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_wall.html b/doc/doc2/fix_wall.html deleted file mode 100644 index 891863492f..0000000000 --- a/doc/doc2/fix_wall.html +++ /dev/null @@ -1,310 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix wall/lj93 command -

    -

    fix wall/lj126 command -

    -

    fix wall/lj1043 command -

    -

    fix wall/colloid command -

    -

    fix wall/harmonic command -

    -

    Syntax: -

    -
    fix ID group-ID style face args ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • style = wall/lj93 or wall/lj126 or wall/lj1043 or wall/colloid or wall/harmonic - -
    • one or more face/arg pairs may be appended - -
    • face = xlo or xhi or ylo or yhi or zlo or zhi - -
        args = coord epsilon sigma cutoff
-    coord = position of wall = EDGE or constant or variable
-      EDGE = current lo or hi edge of simulation box
-      constant = number like 0.0 or -30.0 (distance units)
-      variable = equal-style variable like v_x or v_wiggle
-    epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
-      epsilon can be a variable (see below)
-    sigma = size factor for wall-particle interaction (distance units)
-      sigma can be a variable (see below)
-    cutoff = distance from wall at which wall-particle interaction is cut off (distance units) 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = units or fld - -
        units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units
-  fld value = yes or no
-    yes = invoke the wall constraint to be compatible with implicit FLD
-    no = invoke the wall constraint in the normal way
-  pbc value = yes or no
-    yes = allow periodic boundary in a wall dimension
-    no = require non-perioidic boundaries in any wall dimension 
-
      - -
    -

    Examples: -

    -
    fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
-fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
-fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
-fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 
-
    -

    Description: -

    -

    Bound the simulation domain on one or more of its faces with a flat -wall that interacts with the atoms in the group by generating a force -on the atom in a direction perpendicular to the wall. The energy of -wall-particle interactions depends on the style. -

    -

    For style wall/lj93, the energy E is given by the 9/3 potential: -

    -
    -
    -

    For style wall/lj126, the energy E is given by the 12/6 potential: -

    -
    -
    -

    For style wall/lj1043, the energy E is given by the 10/4/3 potential: -

    -
    -
    -

    For style wall/colloid, the energy E is given by an integrated form -of the pair_style colloid potential: -

    -
    -
    -

    For style wall/harmonic, the energy E is given by a harmonic spring -potential: -

    -
    -
    -

    In all cases, r is the distance from the particle to the wall at -position coord, and Rc is the cutoff distance at which the -particle and wall no longer interact. The energy of the wall -potential is shifted so that the wall-particle interaction energy is -0.0 at the cutoff distance. -

    -

    Up to 6 walls or faces can be specified in a single command: xlo, -xhi, ylo, yhi, zlo, zhi. A lo face interacts with -particles near the lower side of the simulation box in that dimension. -A hi face interacts with particles near the upper side of the -simulation box in that dimension. -

    -

    The position of each wall can be specified in one of 3 ways: as the -EDGE of the simulation box, as a constant value, or as a variable. If -EDGE is used, then the corresponding boundary of the current -simulation box is used. If a numeric constant is specified then the -wall is placed at that position in the appropriate dimension (x, y, or -z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v_name, -where name is an equal-style variable name. In this -case the variable is evaluated each timestep and the result becomes -the current position of the reflecting wall. Equal-style variables -can specify formulas with various mathematical functions, and include -thermo_style command keywords for the simulation -box parameters and timestep and elapsed time. Thus it is easy to -specify a time-dependent wall position. See examples below. -

    -

    For the wall/lj93 and wall/lj126 and wall/lj1043 styles, -epsilon and sigma are the usual Lennard-Jones parameters, which -determine the strength and size of the particle as it interacts with -the wall. Epsilon has energy units. Note that this epsilon and -sigma may be different than any epsilon or sigma values defined -for a pair style that computes particle-particle interactions. -

    -

    The wall/lj93 interaction is derived by integrating over a 3d -half-lattice of Lennard-Jones 12/6 particles. The wall/lj126 -interaction is effectively a harder, more repulsive wall interaction. -The wall/lj1043 interaction is yet a different form of wall -interaction, described in Magda et al in (Magda). -

    -

    For the wall/colloid style, R is the radius of the colloid -particle, D is the distance from the surface of the colloid particle -to the wall (r-R), and sigma is the size of a constituent LJ -particle inside the colloid particle and wall. Note that the cutoff -distance Rc in this case is the distance from the colloid particle -center to the wall. The prefactor epsilon can be thought of as an -effective Hamaker constant with energy units for the strength of the -colloid-wall interaction. More specifically, the epsilon pre-factor -= 4 * pi^2 * rho_wall * rho_colloid * epsilon * sigma^6, where epsilon -and sigma are the LJ parameters for the constituent LJ -particles. Rho_wall and rho_colloid are the number density of the -constituent particles, in the wall and colloid respectively, in units -of 1/volume. -

    -

    The wall/colloid interaction is derived by integrating over -constituent LJ particles of size sigma within the colloid particle -and a 3d half-lattice of Lennard-Jones 12/6 particles of size sigma -in the wall. As mentioned in the preceeding paragraph, the density of -particles in the wall and colloid can be different, as specified by -the epsilon pre-factor. -

    -

    For the wall/harmonic style, epsilon is effectively the spring -constant K, and has units (energy/distance^2). The input parameter -sigma is ignored. The minimum energy position of the harmonic -spring is at the cutoff. This is a repulsive-only spring since the -interaction is truncated at the cutoff -

    -

    For any wall, the epsilon and/or sigma parameter can be specified -as an equal-style variable, in which case it should be -specified as v_name, where name is the variable name. As with a -variable wall position, the variable is evaluated each timestep and -the result becomes the current epsilon or sigma of the wall. -Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent wall interaction. -

    -

    IMPORTANT NOTE: For all of the styles, you must insure that r is -always > 0 for all particles in the group, or LAMMPS will generate an -error. This means you cannot start your simulation with particles at -the wall position coord (r = 0) or with particles on the wrong side -of the wall (r < 0). For the wall/lj93 and wall/lj126 styles, the -energy of the wall/particle interaction (and hence the force on the -particle) blows up as r -> 0. The wall/colloid style is even more -restrictive, since the energy blows up as D = r-R -> 0. This means -the finite-size particles of radius R must be a distance larger than R -from the wall position coord. The harmonic style is a softer -potential and does not blow up as r -> 0, but you must use a large -enough epsilon that particles always reamin on the correct side of -the wall (r > 0). -

    -

    The units keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant or -variable is used. It is not relevant when EDGE is used to specify a -face position. In the variable case, the variable is assumed to -produce a value compatible with the units setting you specify. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacings. -

    -

    The fld keyword can be used with a yes setting to invoke the wall -constraint before pairwise interactions are computed. This allows an -implicit FLD model using pair_style lubricateU -to include the wall force in its calculations. If the setting is -no, wall forces are imposed after pairwise interactions, in the -usual manner. -

    -

    The pbc keyword can be used with a yes setting to allow walls to -be specified in a periodic dimension. See the -boundary command for options on simulation box -boundaries. The default for pbc is no, which means the system -must be non-periodic when using a wall. But you may wish to use a -periodic box. E.g. to allow some particles to interact with the wall -via the fix group-ID, and others to pass through it and wrap around a -periodic box. In this case you should insure that the wall if -sufficiently far enough away from the box boundary. If you do not, -then particles may interact with both the wall and with periodic -images on the other side of the box, which is probably not what you -want. -

    -
    - -

    Here are examples of variable definitions that move the wall position -in a time-dependent fashion using equal-style -variables. The wall interaction parameters (epsilon, -sigma) could be varied with additional variable definitions. -

    -
    variable ramp equal ramp(0,10)
-fix 1 all wall xlo v_ramp 1.0 1.0 2.5 
-
    -
    variable linear equal vdisplace(0,20)
-fix 1 all wall xlo v_linear 1.0 1.0 2.5 
-
    -
    variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 
-
    -
    variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 
-
    -

    The ramp(lo,hi) function adjusts the wall position linearly from lo to -hi over the course of a run. The vdisplace(c0,velocity) function does -something similar using the equation position = c0 + velocity*delta, -where delta is the elapsed time. -

    -

    The swiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, where omega = 2 PI -/ period: -

    -
    position = c0 + A sin(omega*delta) 
-
    -

    The cwiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, which will have an -initial wall velocity of 0.0, and thus may impose a gentler -perturbation on the particles: -

    -
    position = c0 + A (1 - cos(omega*delta)) 
-
    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the energy of interaction between atoms and each wall to -the system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar energy and a global vector of -forces, which can be accessed by various output -commands. Note that the scalar energy is -the sum of interactions with all defined walls. If you want the -energy on a per-wall basis, you need to use multiple fix wall -commands. The length of the vector is equal to the number of walls -defined by the fix. Each vector value is the normal force on a -specific wall. Note that an outward force on a wall will be a -negative value for lo walls and a positive value for hi walls. -The scalar and vector values calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the fix_modify -energy option for this fix. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix wall/reflect, -fix wall/gran, -fix wall/region -

    -

    Default: -

    -

    The option defaults units = lattice, fld = no, and pbc = no. -

    -
    - - - -

    (Magda) Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985); -erratum in JCP 84, 2901 (1986). -

    - diff --git a/doc/doc2/fix_wall_gran.html b/doc/doc2/fix_wall_gran.html deleted file mode 100644 index 032beac914..0000000000 --- a/doc/doc2/fix_wall_gran.html +++ /dev/null @@ -1,176 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix wall/gran command -

    -

    Syntax: -

    -
    fix ID group-ID wall/gran Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • wall/gran = style name of this fix command - -
    • Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) - -
    • Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) - -
    • gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) - -
    • gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) - -
    • xmu = static yield criterion (unitless value between 0.0 and 1.0e4) - -
    • dampflag = 0 or 1 if tangential damping force is excluded or included - -
    • wallstyle = xplane or yplane or zplane or zcylinder - -
    • args = list of arguments for a particular style - -
        xplane or yplane or zplane args = lo hi
-    lo,hi = position of lower and upper plane (distance units), either can be NULL)
-  zcylinder args = radius
-    radius = cylinder radius (distance units) 
-
      -
    • zero or more keyword/value pairs may be appended to args - -
    • keyword = wiggle or shear - -
        wiggle values = dim amplitude period
-    dim = x or y or z
-    amplitude = size of oscillation (distance units)
-    period = time of oscillation (time units)
-  shear values = dim vshear
-    dim = x or y or z
-    vshear = magnitude of shear velocity (velocity units) 
-
      - -
    -

    Examples: -

    -
    fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 
-fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL 
-fix 2 all wall/gran 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 
-
    -

    Description: -

    -

    Bound the simulation domain of a granular system with a frictional -wall. All particles in the group interact with the wall when they are -close enough to touch it. -

    -

    The first set of parameters (Kn, Kt, gamma_n, gamma_t, xmu, and -dampflag) have the same meaning as those specified with the -pair_style granular force fields. This means a NULL -can be used for either Kt or gamma_t as described on that page. If a -NULL is used for Kt, then a default value is used where Kt = 2/7 Kn. -If a NULL is used for gamma_t, then a default value is used where -gamma_t = 1/2 gamma_n. -

    -

    The nature of the wall/particle interactions are determined by which -pair_style is used in your input script: hooke, hooke/history, or -hertz/history. The equation for the force between the wall and -particles touching it is the same as the corresponding equation on the -pair_style granular doc page, in the limit of one of -the two particles going to infinite radius and mass (flat wall). -I.e. delta = radius - r = overlap of particle with wall, m_eff = mass -of particle, and sqrt(RiRj/Ri+Rj) becomes sqrt(radius of particle). -The units for Kn, Kt, gamma_n, and gamma_t are as described on that -doc page. The meaning of xmu and dampflag are also as described on -that page. Note that you can choose different values for these 6 -wall/particle coefficients than for particle/particle interactions, if -you wish your wall to interact differently with the particles, e.g. if -the wall is a different material. -

    -

    IMPORTANT NOTE: As discussed on the doc page for pair_style -granular, versions of LAMMPS before 9Jan09 used a -different equation for Hertzian interactions. This means Hertizian -wall/particle interactions have also changed. They now include a -sqrt(radius) term which was not present before. Also the previous -versions used Kn and Kt from the pairwise interaction and hardwired -dampflag to 1, rather than letting them be specified directly. This -means you can set the values of the wall/particle coefficients -appropriately in the current code to reproduce the results of a -prevoius Hertzian monodisperse calculation. For example, for the -common case of a monodisperse system with particles of diameter 1, Kn, -Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were -previously. -

    -

    The wallstyle can be planar or cylindrical. The 3 planar options -specify a pair of walls in a dimension. Wall positions are given by -lo and hi. Either of the values can be specified as NULL if a -single wall is desired. For a zcylinder wallstyle, the cylinder's -axis is at x = y = 0.0, and the radius of the cylinder is specified. -

    -

    Optionally, the wall can be moving, if the wiggle or shear -keywords are appended. Both keywords cannot be used together. -

    -

    For the wiggle keyword, the wall oscillates sinusoidally, similar to -the oscillations of particles which can be specified by the -fix_move command. This is useful in packing -simulations of granular particles. The arguments to the wiggle -keyword specify a dimension for the motion, as well as it's -amplitude and period. Note that if the dimension is in the plane -of the wall, this is effectively a shearing motion. If the dimension -is perpendicular to the wall, it is more of a shaking motion. A -zcylinder wall can only be wiggled in the z dimension. -

    -

    Each timestep, the position of a wiggled wall in the appropriate dim -is set according to this equation: -

    -
    position = coord + A - A cos (omega * delta) 
-
    -

    where coord is the specified initial position of the wall, A is -the amplitude, omega is 2 PI / period, and delta is the time -elapsed since the fix was specified. The velocity of the wall is set -to the derivative of this expression. -

    -

    For the shear keyword, the wall moves continuously in the specified -dimension with velocity vshear. The dimension must be tangential to -walls with a planar wallstyle, e.g. in the y or z directions for -an xplane wall. For zcylinder walls, a dimension of z means the -cylinder is moving in the z-direction along it's axis. A dimension of -x or y means the cylinder is spinning around the z-axis, either in -the clockwise direction for vshear > 0 or counter-clockwise for -vshear < 0. In this case, vshear is the tangential velocity of -the wall at whatever radius has been defined. -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    This fix writes the shear friction state of atoms interacting with the -wall to binary restart files, so that a simulation can -continue correctly if granular potentials with shear "history" effects -are being used. See the read_restart command for -info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. -

    -

    None of the fix_modify options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various output commands. No -parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Any dimension (xyz) that has a granular wall must be non-periodic. -

    -

    Related commands: -

    -

    fix_move, pair_style granular -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_wall_piston.html b/doc/doc2/fix_wall_piston.html deleted file mode 100644 index b76361ce91..0000000000 --- a/doc/doc2/fix_wall_piston.html +++ /dev/null @@ -1,131 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix wall/piston command -

    -

    Syntax: -

    -
    fix ID group-ID wall/piston face ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • wall/piston = style name of this fix command - -
    • face = zlo - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = pos or vel or ramp or units - -
        pos args = z
-    z = z coordinate at which the piston begins (distance units)
-  vel args = vz
-    vz = final velocity of the piston (velocity units)
-  ramp = use a linear velocity ramp from 0 to vz
-  temp args = target damp seed extent
-    target = target velocity for region immediately ahead of the piston
-    damp = damping paramter (time units)
-    seed = random number seed for langevin kicks
-    extent = extent of thermostated region (distance units)
-  units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    fix xwalls all wall/piston zlo
-fix walls all wall/piston zlo pos 1.0 vel 10.0 units box
-fix top all wall/piston zlo vel 10.0 ramp 
-
    -

    Description: -

    -

    Bound the simulation with a moving wall which reflect particles in the -specified group and drive the system with an effective infinite-mass -piston capable of driving shock waves. -

    -

    A momentum mirror technique is used, which means that if an atom (or -the wall) moves such that an atom is outside the wall on a timestep by -a distance delta (e.g. due to fix nve), then it is put -back inside the face by the same delta, and the velocity relative to -the moving wall is flipped in z. For instance, a stationary particle -hit with a piston wall with velocity vz, will end the timestep with a -velocity of 2*vz. -

    -

    Currently the face keyword can only be zlo. This creates a piston -moving in the positive z direction. Particles with z coordinate less -than the wall position are reflected to a z coordinate greater than -the wall position. If the piston velocity is vpz and the particle -velocity before reflection is vzi, the particle velocity after -reflection is -vzi + 2*vpz. -

    -

    The initial position of the wall can be specified by the pos keyword. -

    -

    The final velocity of the wall can be specified by the vel keyword -

    -

    The ramp keyword will cause the wall/piston to adjust the velocity -linearly from zero velocity to vel over the course of the run. If -the ramp keyword is omitted then the wall/piston moves at a constant -velocity defined by vel. -

    -

    The temp keyword will cause the region immediately in front of the -wall/piston to be thermostated with a Langevin thermostat. This -region moves with the piston. The damping and kicking are measured in -the reference frame of the piston. So, a temperature of zero would -mean all particles were moving at exactly the speed of the -wall/piston. -

    -

    The units keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant is used. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacings. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    The face that has the wall/piston must be boundary type 's' -(shrink-wrapped). The opposing face can be -any boundary type other than periodic. -

    -

    A wall/piston should not be used with rigid bodies such as those -defined by a "fix rigid" command. This is because the wall/piston -displaces atoms directly rather than exerting a force on them. -

    -

    Related commands: -

    -

    fix wall/reflect command, fix -append/atoms command -

    -

    Default: -

    -

    The keyword defaults are pos = 0, vel = 0, units = lattice. -

    - diff --git a/doc/doc2/fix_wall_reflect.html b/doc/doc2/fix_wall_reflect.html deleted file mode 100644 index c57e5d1806..0000000000 --- a/doc/doc2/fix_wall_reflect.html +++ /dev/null @@ -1,199 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix wall/reflect command -

    -

    fix wall/reflect/kk command -

    -

    Syntax: -

    -
    fix ID group-ID wall/reflect face arg ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • wall/reflect = style name of this fix command - -
    • one or more face/arg pairs may be appended - -
    • face = xlo or xhi or ylo or yhi or zlo or zhi - -
        xlo,ylo,zlo arg = EDGE or constant or variable
-    EDGE = current lo edge of simulation box
-    constant = number like 0.0 or -30.0 (distance units)
-    variable = equal-style variable like v_x or v_wiggle
-  xhi,yhi,zhi arg = EDGE or constant or variable
-    EDGE = current hi edge of simulation box
-    constant = number like 50.0 or 100.3 (distance units)
-    variable = equal-style variable like v_x or v_wiggle 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = units - -
        units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    fix xwalls all wall/reflect xlo EDGE xhi EDGE
-fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
-fix top all wall/reflect zhi v_pressdown 
-
    -

    Description: -

    -

    Bound the simulation with one or more walls which reflect particles -in the specified group when they attempt to move thru them. -

    -

    Reflection means that if an atom moves outside the wall on a timestep -by a distance delta (e.g. due to fix nve), then it is -put back inside the face by the same delta, and the sign of the -corresponding component of its velocity is flipped. -

    -

    When used in conjunction with fix nve and run_style -verlet, the resultant time-integration algorithm is -equivalent to the primitive splitting algorithm (PSA) described by -Bond. Because each reflection event divides -the corresponding timestep asymmetrically, energy conservation is only -satisfied to O(dt), rather than to O(dt^2) as it would be for -velocity-Verlet integration without reflective walls. -

    -

    Up to 6 walls or faces can be specified in a single command: xlo, -xhi, ylo, yhi, zlo, zhi. A lo face reflects particles -that move to a coordinate less than the wall position, back in the -hi direction. A hi face reflects particles that move to a -coordinate higher than the wall position, back in the lo direction. -

    -

    The position of each wall can be specified in one of 3 ways: as the -EDGE of the simulation box, as a constant value, or as a variable. If -EDGE is used, then the corresponding boundary of the current -simulation box is used. If a numeric constant is specified then the -wall is placed at that position in the appropriate dimension (x, y, or -z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v_name, -where name is an equal-style variable name. In this -case the variable is evaluated each timestep and the result becomes -the current position of the reflecting wall. Equal-style variables -can specify formulas with various mathematical functions, and include -thermo_style command keywords for the simulation -box parameters and timestep and elapsed time. Thus it is easy to -specify a time-dependent wall position. -

    -

    The units keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant or -variable is used. It is not relevant when EDGE is used to specify a -face position. In the variable case, the variable is assumed to -produce a value compatible with the units setting you specify. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacings. -

    -
    - -

    Here are examples of variable definitions that move the wall position -in a time-dependent fashion using equal-style -variables. -

    -
    variable ramp equal ramp(0,10)
-fix 1 all wall/reflect xlo v_ramp 
-
    -
    variable linear equal vdisplace(0,20)
-fix 1 all wall/reflect xlo v_linear 
-
    -
    variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle  
-
    -
    variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle 
-
    -

    The ramp(lo,hi) function adjusts the wall position linearly from lo to -hi over the course of a run. The vdisplace(c0,velocity) function does -something similar using the equation position = c0 + velocity*delta, -where delta is the elapsed time. -

    -

    The swiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, where omega = 2 PI -/ period: -

    -
    position = c0 + A sin(omega*delta) 
-
    -

    The cwiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, which will have an -initial wall velocity of 0.0, and thus may impose a gentler -perturbation on the particles: -

    -
    position = c0 + A (1 - cos(omega*delta)) 
-
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can -be used with the start/stop keywords of the run command. -This fix is not invoked during energy minimization. -

    -

    Restrictions: -

    -

    Any dimension (xyz) that has a reflecting wall must be non-periodic. -

    -

    A reflecting wall should not be used with rigid bodies such as those -defined by a "fix rigid" command. This is because the wall/reflect -displaces atoms directly rather than exerts a force on them. For -rigid bodies, use a soft wall instead, such as fix -wall/lj93. LAMMPS will flag the use of a rigid -fix with fix wall/reflect with a warning, but will not generate an -error. -

    -

    Related commands: -

    -

    fix wall/lj93, fix oneway -

    -

    Default: none -

    -
    - - - -

    (Bond) Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007). -

    - diff --git a/doc/doc2/fix_wall_region.html b/doc/doc2/fix_wall_region.html deleted file mode 100644 index 9f4a5d06ce..0000000000 --- a/doc/doc2/fix_wall_region.html +++ /dev/null @@ -1,210 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix wall/region command -

    -

    Syntax: -

    -
    fix ID group-ID wall/region region-ID style epsilon sigma cutoff 
-
    -
    • ID, group-ID are documented in fix command -
    • wall/region = style name of this fix command -
    • region-ID = region whose boundary will act as wall -
    • style = lj93 or lj126 or colloid or harmonic -
    • epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) -
    • sigma = size factor for wall-particle interaction (distance units) -
    • cutoff = distance from wall at which wall-particle interaction is cut off (distance units) -
    -

    Examples: -

    -
    fix wall all wall/region mySphere lj93 1.0 1.0 2.5 
-
    -

    Description: -

    -

    Treat the surface of the geometric region defined by the region-ID -as a bounding wall which interacts with nearby particles according to -the specified style. The distance between a particle and the surface -is the distance to the nearest point on the surface and the force the -wall exerts on the particle is along the direction between that point -and the particle, which is the direction normal to the surface at that -point. Note that if the region surface is comprised of multiple -"faces", then each face can exert a force on the particle if it is -close enough. E.g. for region_style block, a particle -in the interior, near a corner of the block, could feel wall forces -from 1, 2, or 3 faces of the block. -

    -

    Regions are defined using the region command. Note that -the region volume can be interior or exterior to the bounding surface, -which will determine in which direction the surface interacts with -particles, i.e. the direction of the surface normal. Regions can -either be primitive shapes (block, sphere, cylinder, etc) or -combinations of primitive shapes specified via the union or -intersect region styles. These latter styles can be used to -construct particle containers with complex shapes. Regions can also -change over time via the region command keywords (move) -and rotate. If such a region is used with this fix, then the of -region surface will move over time in the corresponding manner. -

    -

    IMPORTANT NOTE: As discussed on the region command doc -page, regions in LAMMPS do not get wrapped across periodic boundaries. -It is up to you to insure that periodic or non-periodic boundaries are -specified appropriately via the boundary command when -using a region as a wall that bounds particle motion. This also means -that if you embed a region in your simulation box and want it to -repulse particles from its surface (using the "side out" option in the -region command), that its repulsive force will not be -felt across a periodic boundary. -

    -

    IMPORTANT NOTE: For primitive regions with sharp corners and/or edges -(e.g. a block or cylinder), wall/particle forces are computed -accurately for both interior and exterior regions. For union and -intersect regions, additional sharp corners and edges may be present -due to the intersection of the surfaces of 2 or more primitive -volumes. These corners and edges can be of two types: concave or -convex. Concave points/edges are like the corners of a cube as seen -by particles in the interior of a cube. Wall/particle forces around -these features are computed correctly. Convex points/edges are like -the corners of a cube as seen by particles exterior to the cube, -i.e. the points jut into the volume where particles are present. -LAMMPS does NOT compute the location of these convex points directly, -and hence wall/particle forces in the cutoff volume around these -points suffer from inaccuracies. The basic problem is that the -outward normal of the surface is not continuous at these points. This -can cause particles to feel no force (they don't "see" the wall) when -in one location, then move a distance epsilon, and suddenly feel a -large force because they now "see" the wall. In a worst-case -scenario, this can blow particles out of the simulation box. Thus, as -a general rule you should not use the fix wall/region command with -union or interesect regions that have convex points or edges. -

    -

    IMPORTANT NOTE: Similarly, you should not define union or -intersert regions for use with this command that share a common -face, even if the face is smooth. E.g. two regions of style block in -a union region, where the two blocks have the same face. This is -because LAMMPS discards points that are part of multiple sub-regions -when calculating wall/particle interactions, to avoid double-counting -the interaction. Having two coincident faces could cause the face to -become invisible to the particles. The solution is to make the two -faces differ by epsilon in their position. -

    -

    The energy of wall-particle interactions depends on the specified -style. -

    -

    For style lj93, the energy E is given by the 9/3 potential: -

    -
    -
    -

    For style lj126, the energy E is given by the 12/6 potential: -

    -
    -
    -

    For style colloid, the energy E is given by an integrated form of -the pair_style colloid potential: -

    -
    -
    -

    For style wall/harmonic, the energy E is given by a harmonic spring -potential: -

    -
    -
    -

    In all cases, r is the distance from the particle to the region -surface, and Rc is the cutoff distance at which the particle and -surface no longer interact. The energy of the wall potential is -shifted so that the wall-particle interaction energy is 0.0 at the -cutoff distance. -

    -

    For the lj93 and lj126 styles, epsilon and sigma are the usual -Lennard-Jones parameters, which determine the strength and size of the -particle as it interacts with the wall. Epsilon has energy units. -Note that this epsilon and sigma may be different than any -epsilon or sigma values defined for a pair style that computes -particle-particle interactions. -

    -

    The lj93 interaction is derived by integrating over a 3d -half-lattice of Lennard-Jones 12/6 particles. The lj126 interaction -is effectively a harder, more repulsive wall interaction. -

    -

    For the colloid style, epsilon is effectively a Hamaker constant -with energy units for the colloid-wall interaction, R is the radius -of the colloid particle, D is the distance from the surface of the -colloid particle to the wall (r-R), and sigma is the size of a -constituent LJ particle inside the colloid particle. Note that the -cutoff distance Rc in this case is the distance from the colloid -particle center to the wall. -

    -

    The colloid interaction is derived by integrating over constituent -LJ particles of size sigma within the colloid particle and a 3d -half-lattice of Lennard-Jones 12/6 particles of size sigma in the -wall. -

    -

    For the wall/harmonic style, epsilon is effectively the spring -constant K, and has units (energy/distance^2). The input parameter -sigma is ignored. The minimum energy position of the harmonic -spring is at the cutoff. This is a repulsive-only spring since the -interaction is truncated at the cutoff -

    -

    IMPORTANT NOTE: For all of the styles, you must insure that r is -always > 0 for all particles in the group, or LAMMPS will generate an -error. This means you cannot start your simulation with particles on -the region surface (r = 0) or with particles on the wrong side of the -region surface (r < 0). For the wall/lj93 and wall/lj126 styles, -the energy of the wall/particle interaction (and hence the force on -the particle) blows up as r -> 0. The wall/colloid style is even -more restrictive, since the energy blows up as D = r-R -> 0. This -means the finite-size particles of radius R must be a distance larger -than R from the region surface. The harmonic style is a softer -potential and does not blow up as r -> 0, but you must use a large -enough epsilon that particles always reamin on the correct side of -the region surface (r > 0). -

    -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. -

    -

    The fix_modify energy option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of thermodynamic -output. -

    -

    This fix computes a global scalar energy and a global 3-length vector -of forces, which can be accessed by various output -commands. The scalar energy is the sum -of energy interactions for all particles interacting with the wall -represented by the region surface. The 3 vector quantities are the -x,y,z components of the total force acting on the wall due to the -particles. The scalar and vector values calculated by this fix are -"extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. -

    -

    The forces due to this fix are imposed during an energy minimization, -invoked by the minimize command. -

    -

    IMPORTANT NOTE: If you want the atom/wall interaction energy to be -included in the total potential energy of the system (the quantity -being minimized), you MUST enable the fix_modify -energy option for this fix. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix wall/lj93, -fix wall/lj126, -fix wall/colloid, -fix wall/gran -

    -

    Default: none -

    - diff --git a/doc/doc2/fix_wall_srd.html b/doc/doc2/fix_wall_srd.html deleted file mode 100644 index ea3f64c68b..0000000000 --- a/doc/doc2/fix_wall_srd.html +++ /dev/null @@ -1,203 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    fix wall/srd command -

    -

    Syntax: -

    -
    fix ID group-ID wall/srd face arg ... keyword value ... 
-
    -
    • ID, group-ID are documented in fix command - -
    • wall/srd = style name of this fix command - -
    • one or more face/arg pairs may be appended - -
    • face = xlo or xhi or ylo or yhi or zlo or zhi - -
        xlo,ylo,zlo arg = EDGE or constant or variable
-    EDGE = current lo edge of simulation box
-    constant = number like 0.0 or -30.0 (distance units)
-    variable = equal-style variable like v_x or v_wiggle
-  xhi,yhi,zhi arg = EDGE or constant or variable
-    EDGE = current hi edge of simulation box
-    constant = number like 50.0 or 100.3 (distance units)
-    variable = equal-style variable like v_x or v_wiggle 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = units - -
        units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units 
-
      - -
    -

    Examples: -

    -
    fix xwalls all wall/srd xlo EDGE xhi EDGE
-fix walls all wall/srd xlo 0.0 ylo 10.0 units box
-fix top all wall/srd zhi v_pressdown 
-
    -

    Description: -

    -

    Bound the simulation with one or more walls which interact with -stochastic reaction dynamics (SRD) particles as slip (smooth) or -no-slip (rough) flat surfaces. The wall interaction is actually -invoked via the fix srd command, only on the group of -SRD particles it defines, so the group setting for the fix wall/srd -command is ignored. -

    -

    A particle/wall collision occurs if an SRD particle moves outside the -wall on a timestep. This alters the position and velocity of the SRD -particle and imparts a force to the wall. -

    -

    The collision and Tsrd settings specified via the fix -srd command affect the SRD/wall collisions. A slip -setting for the collision keyword means that the tangential -component of the SRD particle momentum is preserved. Thus only a -normal force is imparted to the wall. The normal component of the new -SRD velocity is sampled from a Gaussian distribution at temperature -Tsrd. -

    -

    For a noslip setting of the collision keyword, both the normal and -tangential components of the new SRD velocity are sampled from a -Gaussian distribution at temperature Tsrd. Additionally, a new -tangential direction for the SRD velocity is chosen randomly. This -collision style imparts both a normal and tangential force to the -wall. -

    -

    Up to 6 walls or faces can be specified in a single command: xlo, -xhi, ylo, yhi, zlo, zhi. A lo face reflects particles -that move to a coordinate less than the wall position, back in the -hi direction. A hi face reflects particles that move to a -coordinate higher than the wall position, back in the lo direction. -

    -

    The position of each wall can be specified in one of 3 ways: as the -EDGE of the simulation box, as a constant value, or as a variable. If -EDGE is used, then the corresponding boundary of the current -simulation box is used. If a numeric constant is specified then the -wall is placed at that position in the appropriate dimension (x, y, or -z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v_name, -where name is an equal-style variable name. In this -case the variable is evaluated each timestep and the result becomes -the current position of the reflecting wall. Equal-style variables -can specify formulas with various mathematical functions, and include -thermo_style command keywords for the simulation -box parameters and timestep and elapsed time. Thus it is easy to -specify a time-dependent wall position. -

    -

    IMPORTANT NOTE: Because the trajectory of the SRD particle is tracked -as it collides with the wall, you must insure that r = distance of the -particle from the wall, is always > 0 for SRD particles, or LAMMPS -will generate an error. This means you cannot start your simulation -with SRD particles at the wall position coord (r = 0) or with -particles on the wrong side of the wall (r < 0). -

    -

    IMPORTANT NOTE: If you have 2 or more walls that come together at an -edge or corner (e.g. walls in the x and y dimensions), then be sure to -set the overlap keyword to yes in the fix srd -command, since the walls effectively overlap when SRD particles -collide with them. LAMMPS will issue a warning if you do not do this. -

    -

    IMPORTANT NOTE: The walls of this fix only interact with SRD -particles, as defined by the fix srd command. If you -are simulating a mixture containing other kinds of particles, then you -should typically use another wall command to act on -the other particles. Since SRD particles will be colliding both with -the walls and the other particles, it is important to insure that the -other particle's finite extent does not overlap an SRD wall. If you -do not do this, you may generate errors when SRD particles end up -"inside" another particle or a wall at the beginning of a collision -step. -

    -

    The units keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant is used. -It is not relevant when EDGE or a variable is used to specify a face -position. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacings. -

    -
    - -

    Here are examples of variable definitions that move the wall position -in a time-dependent fashion using equal-style -variables. -

    -
    variable ramp equal ramp(0,10)
-fix 1 all wall/srd xlo v_ramp 
-
    -
    variable linear equal vdisplace(0,20)
-fix 1 all wall/srd xlo v_linear 
-
    -
    variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall/srd xlo v_wiggle  
-
    -
    variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall/srd xlo v_wiggle 
-
    -

    The ramp(lo,hi) function adjusts the wall position linearly from lo to -hi over the course of a run. The displace(c0,velocity) function does -something similar using the equation position = c0 + velocity*delta, -where delta is the elapsed time. -

    -

    The swiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, where omega = 2 PI -/ period: -

    -
    position = c0 + A sin(omega*delta) 
-
    -

    The cwiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, which will have an -initial wall velocity of 0.0, and thus may impose a gentler -perturbation on the particles: -

    -
    position = c0 + A (1 - cos(omega*delta)) 
-
    -
    - -

    Restart, fix_modify, output, run start/stop, minimize info: -

    -

    No information about this fix is written to binary restart -files. None of the fix_modify options -are relevant to this fix. -

    -

    This fix computes a global array of values which can be accessed by -various output commands. The number of -rows in the array is equal to the number of walls defined by the fix. -The number of columns is 3, for the x,y,z components of force on each -wall. -

    -

    Note that an outward normal force on a wall will be a negative value -for lo walls and a positive value for hi walls. The array values -calculated by this fix are "extensive". -

    -

    No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

    -

    Restrictions: -

    -

    Any dimension (xyz) that has an SRD wall must be non-periodic. -

    -

    Related commands: -

    -

    fix srd -

    -

    Default: none -

    - diff --git a/doc/doc2/genindex.html b/doc/doc2/genindex.html deleted file mode 100644 index 6211380787..0000000000 --- a/doc/doc2/genindex.html +++ /dev/null @@ -1,2244 +0,0 @@ - - - - - - - - - - - - Index — LAMMPS 15 May 2015 version documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    - - - - -
    - - - - - - -
    -
    -
    - -
    - -
    -
    -
    - - -

    Index

    - -
    - A - | B - | C - | D - | E - | F - | G - | I - | J - | K - | L - | M - | N - | P - | Q - | R - | S - | T - | U - | V - | W - -
    -

    A

    - - - -
    - -
    angle_coeff -
    - - -
    angle_style -
    - - -
    angle_style charmm -
    - - -
    angle_style class2 -
    - - -
    angle_style cosine -
    - - -
    angle_style cosine/delta -
    - - -
    angle_style cosine/periodic -
    - - -
    angle_style cosine/shift -
    - - -
    angle_style cosine/shift/exp -
    - - -
    angle_style cosine/squared -
    - - -
    angle_style dipole -
    - -
    - -
    angle_style fourier -
    - - -
    angle_style fourier/simple -
    - - -
    angle_style harmonic -
    - - -
    angle_style hybrid -
    - - -
    angle_style none -
    - - -
    angle_style quartic -
    - - -
    angle_style sdk -
    - - -
    angle_style table -
    - - -
    atom_modify -
    - - -
    atom_style -
    - -
    - -

    B

    - - - -
    - -
    balance -
    - - -
    bond_coeff -
    - - -
    bond_style -
    - - -
    bond_style class2 -
    - - -
    bond_style fene -
    - - -
    bond_style fene/expand -
    - - -
    bond_style harmonic -
    - - -
    bond_style harmonic/shift -
    - - -
    bond_style harmonic/shift/cut -
    - -
    - -
    bond_style hybrid -
    - - -
    bond_style morse -
    - - -
    bond_style none -
    - - -
    bond_style nonlinear -
    - - -
    bond_style quartic -
    - - -
    bond_style table -
    - - -
    boundary -
    - - -
    box -
    - -
    - -

    C

    - - - -
    - -
    change_box -
    - - -
    clear -
    - - -
    comm_modify -
    - - -
    comm_style -
    - - -
    compute -
    - - -
    compute ackland/atom -
    - - -
    compute angle/local -
    - - -
    compute angmom/chunk -
    - - -
    compute basal/atom -
    - - -
    compute body/local -
    - - -
    compute bond/local -
    - - -
    compute centro/atom -
    - - -
    compute chunk/atom -
    - - -
    compute cluster/atom -
    - - -
    compute cna/atom -
    - - -
    compute com -
    - - -
    compute com/chunk -
    - - -
    compute contact/atom -
    - - -
    compute coord/atom -
    - - -
    compute damage/atom -
    - - -
    compute dihedral/local -
    - - -
    compute dilatation/atom -
    - - -
    compute displace/atom -
    - - -
    compute erotate/asphere -
    - - -
    compute erotate/rigid -
    - - -
    compute erotate/sphere -
    - - -
    compute erotate/sphere/atom -
    - - -
    compute event/displace -
    - - -
    compute fep -
    - - -
    compute force/tally -
    - - -
    compute group/group -
    - - -
    compute gyration -
    - - -
    compute gyration/chunk -
    - - -
    compute heat/flux -
    - - -
    compute hexorder/atom -
    - - -
    compute improper/local -
    - - -
    compute inertia/chunk -
    - - -
    compute ke -
    - - -
    compute ke/atom -
    - - -
    compute ke/atom/eff -
    - - -
    compute ke/eff -
    - - -
    compute ke/rigid -
    - - -
    compute meso_e/atom -
    - - -
    compute meso_rho/atom -
    - - -
    compute meso_t/atom -
    - - -
    compute msd -
    - - -
    compute msd/chunk -
    - - -
    compute msd/nongauss -
    - - -
    compute omega/chunk -
    - - -
    compute orientorder/atom -
    - - -
    compute pair -
    - - -
    compute pair/local -
    - - -
    compute pe -
    - - -
    compute pe/atom -
    - - -
    compute plasticity/atom -
    - -
    - -
    compute pressure -
    - - -
    compute property/atom -
    - - -
    compute property/chunk -
    - - -
    compute property/local -
    - - -
    compute rdf -
    - - -
    compute reduce -
    - - -
    compute saed -
    - - -
    compute slice -
    - - -
    compute smd/contact_radius -
    - - -
    compute smd/damage -
    - - -
    compute smd/hourglass_error -
    - - -
    compute smd/internal_energy -
    - - -
    compute smd/plastic_strain -
    - - -
    compute smd/plastic_strain_rate -
    - - -
    compute smd/rho -
    - - -
    compute smd/tlsph_defgrad -
    - - -
    compute smd/tlsph_dt -
    - - -
    compute smd/tlsph_num_neighs -
    - - -
    compute smd/tlsph_shape -
    - - -
    compute smd/tlsph_strain -
    - - -
    compute smd/tlsph_strain_rate -
    - - -
    compute smd/tlsph_stress -
    - - -
    compute smd/ulsph_num_neighs -
    - - -
    compute smd/ulsph_strain -
    - - -
    compute smd/ulsph_strain_rate -
    - - -
    compute smd/ulsph_stress -
    - - -
    compute smd/vol -
    - - -
    compute sna/atom -
    - - -
    compute stress/atom -
    - - -
    compute temp -
    - - -
    compute temp/asphere -
    - - -
    compute temp/chunk -
    - - -
    compute temp/com -
    - - -
    compute temp/cs -
    - - -
    compute temp/deform -
    - - -
    compute temp/deform/eff -
    - - -
    compute temp/drude -
    - - -
    compute temp/eff -
    - - -
    compute temp/partial -
    - - -
    compute temp/profile -
    - - -
    compute temp/ramp -
    - - -
    compute temp/region -
    - - -
    compute temp/region/eff -
    - - -
    compute temp/rotate -
    - - -
    compute temp/sphere -
    - - -
    compute ti -
    - - -
    compute torque/chunk -
    - - -
    compute vacf -
    - - -
    compute vcm/chunk -
    - - -
    compute voronoi/atom -
    - - -
    compute xrd -
    - - -
    compute_modify -
    - - -
    create_atoms -
    - - -
    create_bonds -
    - - -
    create_box -
    - -
    - -

    D

    - - - -
    - -
    delete_atoms -
    - - -
    delete_bonds -
    - - -
    dielectric -
    - - -
    dihedral_coeff -
    - - -
    dihedral_style -
    - - -
    dihedral_style charmm -
    - - -
    dihedral_style class2 -
    - - -
    dihedral_style cosine/shift/exp -
    - - -
    dihedral_style fourier -
    - - -
    dihedral_style harmonic -
    - - -
    dihedral_style helix -
    - - -
    dihedral_style hybrid -
    - - -
    dihedral_style multi/harmonic -
    - -
    - -
    dihedral_style nharmonic -
    - - -
    dihedral_style none -
    - - -
    dihedral_style opls -
    - - -
    dihedral_style quadratic -
    - - -
    dihedral_style table -
    - - -
    dimension -
    - - -
    displace_atoms -
    - - -
    dump -
    - - -
    dump h5md -
    - - -
    dump image -
    - - -
    dump molfile -
    - - -
    dump_modify -
    - -
    - -

    E

    - - -
    - -
    echo -
    - -
    - -

    F

    - - - -
    - -
    fix -
    - - -
    fix adapt -
    - - -
    fix adapt/fep -
    - - -
    fix addforce -
    - - -
    fix addtorque -
    - - -
    fix append/atoms -
    - - -
    fix atc -
    - - -
    fix atom/swap -
    - - -
    fix ave/atom -
    - - -
    fix ave/chunk -
    - - -
    fix ave/correlate -
    - - -
    fix ave/correlate/long -
    - - -
    fix ave/histo -
    - - -
    fix ave/spatial -
    - - -
    fix ave/spatial/sphere -
    - - -
    fix ave/time -
    - - -
    fix aveforce -
    - - -
    fix balance -
    - - -
    fix bond/break -
    - - -
    fix bond/create -
    - - -
    fix bond/swap -
    - - -
    fix box/relax -
    - - -
    fix colvars -
    - - -
    fix deform -
    - - -
    fix deposit -
    - - -
    fix drag -
    - - -
    fix drude -
    - - -
    fix drude/transform/direct -
    - - -
    fix dt/reset -
    - - -
    fix efield -
    - - -
    fix enforce2d -
    - - -
    fix evaporate -
    - - -
    fix external -
    - - -
    fix freeze -
    - - -
    fix gcmc -
    - - -
    fix gld -
    - - -
    fix gle -
    - - -
    fix gravity -
    - - -
    fix heat -
    - - -
    fix imd -
    - - -
    fix indent -
    - - -
    fix ipi -
    - - -
    fix langevin -
    - - -
    fix langevin/drude -
    - - -
    fix langevin/eff -
    - - -
    fix lb/fluid -
    - - -
    fix lb/momentum -
    - - -
    fix lb/pc -
    - - -
    fix lb/rigid/pc/sphere -
    - - -
    fix lb/viscous -
    - - -
    fix lineforce -
    - - -
    fix meso -
    - - -
    fix meso/stationary -
    - - -
    fix momentum -
    - - -
    fix move -
    - - -
    fix msst -
    - - -
    fix neb -
    - - -
    fix nph/asphere -
    - - -
    fix nph/sphere -
    - - -
    fix nphug -
    - - -
    fix npt/asphere -
    - - -
    fix npt/sphere -
    - - -
    fix nve -
    - - -
    fix nve/asphere -
    - - -
    fix nve/asphere/noforce -
    - - -
    fix nve/body -
    - - -
    fix nve/eff -
    - - -
    fix nve/limit -
    - -
    - -
    fix nve/line -
    - - -
    fix nve/noforce -
    - - -
    fix nve/sphere -
    - - -
    fix nve/tri -
    - - -
    fix nvt -
    - - -
    fix nvt/asphere -
    - - -
    fix nvt/eff -
    - - -
    fix nvt/sllod -
    - - -
    fix nvt/sllod/eff -
    - - -
    fix nvt/sphere -
    - - -
    fix oneway -
    - - -
    fix orient/fcc -
    - - -
    fix phonon -
    - - -
    fix pimd -
    - - -
    fix planeforce -
    - - -
    fix pour -
    - - -
    fix press/berendsen -
    - - -
    fix print -
    - - -
    fix property/atom -
    - - -
    fix qbmsst -
    - - -
    fix qeq/comb -
    - - -
    fix qeq/point -
    - - -
    fix qeq/reax -
    - - -
    fix qmmm -
    - - -
    fix qtb -
    - - -
    fix reax/bonds -
    - - -
    fix reax/c/species -
    - - -
    fix recenter -
    - - -
    fix restrain -
    - - -
    fix rigid -
    - - -
    fix saed/vtk -
    - - -
    fix setforce -
    - - -
    fix shake -
    - - -
    fix smd -
    - - -
    fix smd/adjust_dt -
    - - -
    fix smd/integrate_tlsph -
    - - -
    fix smd/integrate_ulsph -
    - - -
    fix smd/move_tri_surf -
    - - -
    fix smd/setvel -
    - - -
    fix smd/wall_surface -
    - - -
    fix spring -
    - - -
    fix spring/rg -
    - - -
    fix spring/self -
    - - -
    fix srd -
    - - -
    fix store/force -
    - - -
    fix store/state -
    - - -
    fix temp/berendsen -
    - - -
    fix temp/csvr -
    - - -
    fix temp/rescale -
    - - -
    fix temp/rescale/eff -
    - - -
    fix tfmc -
    - - -
    fix thermal/conductivity -
    - - -
    fix ti/rs -
    - - -
    fix ti/spring -
    - - -
    fix tmd -
    - - -
    fix ttm -
    - - -
    fix tune/kspace -
    - - -
    fix vector -
    - - -
    fix viscosity -
    - - -
    fix viscous -
    - - -
    fix wall/gran -
    - - -
    fix wall/lj93 -
    - - -
    fix wall/piston -
    - - -
    fix wall/reflect -
    - - -
    fix wall/region -
    - - -
    fix wall/srd -
    - - -
    fix_modify -
    - -
    - -

    G

    - - - -
    - -
    group -
    - -
    - -
    group2ndx -
    - -
    - -

    I

    - - - -
    - -
    if -
    - - -
    improper_coeff -
    - - -
    improper_style -
    - - -
    improper_style class2 -
    - - -
    improper_style cossq -
    - - -
    improper_style cvff -
    - - -
    improper_style fourier -
    - -
    - -
    improper_style harmonic -
    - - -
    improper_style hybrid -
    - - -
    improper_style none -
    - - -
    improper_style ring -
    - - -
    improper_style umbrella -
    - - -
    include -
    - - -
    info -
    - -
    - -

    J

    - - -
    - -
    jump -
    - -
    - -

    K

    - - - -
    - -
    kspace_modify -
    - -
    - -
    kspace_style -
    - -
    - -

    L

    - - - -
    - -
    label -
    - - -
    lattice -
    - -
    - -
    log -
    - -
    - -

    M

    - - - -
    - -
    mass -
    - - -
    min_modify -
    - - -
    min_style -
    - -
    - -
    minimize -
    - - -
    molecule -
    - -
    - -

    N

    - - - -
    - -
    neb -
    - - -
    neigh_modify -
    - - -
    neighbor -
    - -
    - -
    newton -
    - - -
    next -
    - -
    - -

    P

    - - - -
    - -
    package -
    - - -
    pair_coeff -
    - - -
    pair_modify -
    - - -
    pair_style -
    - - -
    pair_style adp -
    - - -
    pair_style airebo -
    - - -
    pair_style awpmd/cut -
    - - -
    pair_style beck -
    - - -
    pair_style body -
    - - -
    pair_style bop -
    - - -
    pair_style born -
    - - -
    pair_style born/coul/long/cs -
    - - -
    pair_style brownian -
    - - -
    pair_style buck -
    - - -
    pair_style buck/long/coul/long -
    - - -
    pair_style colloid -
    - - -
    pair_style comb -
    - - -
    pair_style coul/cut -
    - - -
    pair_style coul/diel -
    - - -
    pair_style dpd -
    - - -
    pair_style dsmc -
    - - -
    pair_style eam -
    - - -
    pair_style edip -
    - - -
    pair_style eff/cut -
    - - -
    pair_style eim -
    - - -
    pair_style gauss -
    - - -
    pair_style gayberne -
    - - -
    pair_style gran/hooke -
    - - -
    pair_style hbond/dreiding/lj -
    - - -
    pair_style hybrid -
    - - -
    pair_style kim -
    - - -
    pair_style lcbop -
    - - -
    pair_style line/lj -
    - - -
    pair_style list -
    - - -
    pair_style lj/charmm/coul/charmm -
    - - -
    pair_style lj/class2 -
    - - -
    pair_style lj/cubic -
    - - -
    pair_style lj/cut -
    - - -
    pair_style lj/cut/dipole/cut -
    - - -
    pair_style lj/cut/soft -
    - - -
    pair_style lj/expand -
    - - -
    pair_style lj/gromacs -
    - - -
    pair_style lj/long/coul/long -
    - - -
    pair_style lj/sdk -
    - - -
    pair_style lj/sf -
    - - -
    pair_style lj/smooth -
    - - -
    pair_style lj/smooth/linear -
    - -
    - -
    pair_style lj96/cut -
    - - -
    pair_style lubricate -
    - - -
    pair_style lubricateU -
    - - -
    pair_style meam -
    - - -
    pair_style mgpt -
    - - -
    pair_style mie/cut -
    - - -
    pair_style morse -
    - - -
    pair_style nb3b/harmonic -
    - - -
    pair_style nm/cut -
    - - -
    pair_style none -
    - - -
    pair_style peri/pmb -
    - - -
    pair_style polymorphic -
    - - -
    pair_style quip -
    - - -
    pair_style reax -
    - - -
    pair_style reax/c -
    - - -
    pair_style resquared -
    - - -
    pair_style smd/hertz -
    - - -
    pair_style smd/tlsph -
    - - -
    pair_style smd/tri_surface -
    - - -
    pair_style smd/ulsph -
    - - -
    pair_style smtbq -
    - - -
    pair_style snap -
    - - -
    pair_style soft -
    - - -
    pair_style sph/heatconduction -
    - - -
    pair_style sph/idealgas -
    - - -
    pair_style sph/lj -
    - - -
    pair_style sph/rhosum -
    - - -
    pair_style sph/taitwater -
    - - -
    pair_style sph/taitwater/morris -
    - - -
    pair_style srp -
    - - -
    pair_style sw -
    - - -
    pair_style table -
    - - -
    pair_style tersoff -
    - - -
    pair_style tersoff/mod -
    - - -
    pair_style tersoff/zbl -
    - - -
    pair_style thole -
    - - -
    pair_style tri/lj -
    - - -
    pair_style vashishta -
    - - -
    pair_style yukawa -
    - - -
    pair_style yukawa/colloid -
    - - -
    pair_style zbl -
    - - -
    pair_write -
    - - -
    partition -
    - - -
    prd -
    - - -
    print -
    - - -
    processors -
    - - -
    python -
    - -
    - -

    Q

    - - -
    - -
    quit -
    - -
    - -

    R

    - - - -
    - -
    read_data -
    - - -
    read_dump -
    - - -
    read_restart -
    - - -
    region -
    - - -
    replicate -
    - -
    - -
    rerun -
    - - -
    reset_timestep -
    - - -
    restart -
    - - -
    run -
    - - -
    run_style -
    - -
    - -

    S

    - - - -
    - -
    set -
    - - -
    shell -
    - -
    - -
    special_bonds -
    - - -
    suffix -
    - -
    - -

    T

    - - - -
    - -
    tad -
    - - -
    temper -
    - - -
    thermo -
    - - -
    thermo_modify -
    - -
    - -
    thermo_style -
    - - -
    timer -
    - - -
    timestep -
    - -
    - -

    U

    - - - -
    - -
    uncompute -
    - - -
    undump -
    - -
    - -
    unfix -
    - - -
    units -
    - -
    - -

    V

    - - - -
    - -
    variable -
    - -
    - -
    velocity -
    - -
    - -

    W

    - - - -
    - -
    write_data -
    - - -
    write_dump -
    - -
    - -
    write_restart -
    - -
    - - - -
    -
    - - -
    -
    - -
    - -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/doc/doc2/group.html b/doc/doc2/group.html deleted file mode 100644 index 53347eefcc..0000000000 --- a/doc/doc2/group.html +++ /dev/null @@ -1,289 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    group command -

    -

    Syntax: -

    -
    group ID style args 
-
    -
    • ID = user-defined name of the group - -
    • style = delete or region or type or id or molecule or variable or include or subtract or union or intersect or dynamic or static - -
        delete = no args
-  clear = no args
-  region args = region-ID
-  type or id or molecule
-    args = list of one or more atom types, atom IDs, or molecule IDs
-      any entry in list can be a sequence formatted as A:B or A:B:C where
-      A = starting index, B = ending index,
-      C = increment between indices, 1 if not specified
-    args = logical value
-      logical = "<" or "<=" or ">" or ">=" or "==" or "!="
-      value = an atom type or atom ID or molecule ID (depending on style)
-    args = logical value1 value2
-      logical = "<>"
-      value1,value2 = atom types or atom IDs or molecule IDs (depending on style)
-  variable args = variable-name
-  include args = molecule
-    molecule = add atoms to group with same molecule ID as atoms already in group
-  subtract args = two or more group IDs
-  union args = one or more group IDs
-  intersect args = two or more group IDs
-  dynamic args = parent-ID keyword value ...
-    one or more keyword/value pairs may be appended
-    keyword = region or var or every
-      region value = region-ID
-      var value = name of variable
-      every value = N = update group every this many timesteps
-  static = no args 
-
      - -
    -

    Examples: -

    -
    group edge region regstrip
-group water type 3 4
-group sub id 10 25 50
-group sub id 10 25 50 500:1000
-group sub id 100:10000:10
-group sub id <= 150
-group polyA molecule <> 50 250
-group hienergy variable eng
-group hienergy include molecule
-group boundary subtract all a2 a3
-group boundary union lower upper
-group boundary intersect upper flow
-group boundary delete
-group mine dynamic all region myRegion every 100 
-
    -

    Description: -

    -

    Identify a collection of atoms as belonging to a group. The group ID -can then be used in other commands such as fix, -compute, dump, or velocity -to act on those atoms together. -

    -

    If the group ID already exists, the group command adds the specified -atoms to the group. -

    -

    IMPORTANT NOTE: By default groups are static, meaning the atoms are -permanently assigned to the group. For example, if the region style -is used to assign atoms to a group, the atoms will remain in the group -even if they later move out of the region. As explained below, the -dynamic style can be used to make a group dynamic so that a periodic -determination is made as to which atoms are in the group. Since many -LAMMPS commands operate on groups of atoms, you should think carefully -about whether making a group dynamic makes sense for your model. -

    -

    A group with the ID all is predefined. All atoms belong to this -group. This group cannot be deleted, or made dynamic. -

    -

    The delete style removes the named group and un-assigns all atoms -that were assigned to that group. Since there is a restriction (see -below) that no more than 32 groups can be defined at any time, the -delete style allows you to remove groups that are no longer needed, -so that more can be specified. You cannot delete a group if it has -been used to define a current fix or compute -or dump. -

    -

    The clear style un-assigns all atoms that were assigned to that -group. This may be dangerous to do during a simulation run, -e.g. using the run every command if a fix or compute or -other operation expects the atoms in the group to remain constant, but -LAMMPS does not check for this. -

    -

    The region style puts all atoms in the region volume into the group. -Note that this is a static one-time assignment. The atoms remain -assigned (or not assigned) to the group even in they later move out of -the region volume. -

    -

    The type, id, and molecule styles put all atoms with the -specified atom types, atom IDs, or molecule IDs into the group. These -3 styles can use arguments specified in one of two formats. -

    -

    The first format is a list of values (types or IDs). For example, the -2nd command in the examples above puts all atoms of type 3 or 4 into -the group named water. Each entry in the list can be a -colon-separated sequence A:B or A:B:C, as in two of the examples -above. A "sequence" generates a sequence of values (types or IDs), -with an optional increment. The first example with 500:1000 has the -default increment of 1 and would add all atom IDs from 500 to 1000 -(inclusive) to the group sub, along with 10,25,50 since they also -appear in the list of values. The second example with 100:10000:10 -uses an increment of 10 and would thus would add atoms IDs -100,110,120, ... 9990,10000 to the group sub. -

    -

    The second format is a logical followed by one or two values (type -or ID). The 7 valid logicals are listed above. All the logicals -except <> take a single argument. The 3rd example above adds all -atoms with IDs from 1 to 150 to the group named sub. The logical <> -means "between" and takes 2 arguments. The 4th example above adds all -atoms belonging to molecules with IDs from 50 to 250 (inclusive) to -the group named polyA. -

    -

    The variable style evaluates a variable to determine which atoms to -add to the group. It must be an atom-style variable -previously defined in the input script. If the variable evaluates -to a non-zero value for a particular atom, then that atom is added -to the specified group. -

    -

    Atom-style variables can specify formulas that include thermodynamic -quantities, per-atom values such as atom coordinates, or per-atom -quantities calculated by computes, fixes, or other variables. They -can also include Boolean logic where 2 numeric values are compared to -yield a 1 or 0 (effectively a true or false). Thus using the -variable style, is a general way to flag specific atoms to include -or exclude from a group. -

    -

    For example, these lines define a variable "eatom" that calculates the -potential energy of each atom and includes it in the group if its -potential energy is above the threshhold value -3.0. -

    -
    compute         1 all pe/atom
-compute         2 all reduce sum c_1
-thermo_style    custom step temp pe c_2
-run             0 
-
    -
    variable        eatom atom "c_1 > -3.0"
-group           hienergy variable eatom 
-
    -

    Note that these lines -

    -
    compute         2 all reduce sum c_1
-thermo_style    custom step temp pe c_2
-run             0 
-
    -

    are necessary to insure that the "eatom" variable is current when the -group command invokes it. Because the eatom variable computes the -per-atom energy via the pe/atom compute, it will only be current if a -run has been performed which evaluated pairwise energies, and the -pe/atom compute was actually invoked during the run. Printing the -thermodyanmic info for compute 2 insures that this is the case, since -it sums the pe/atom compute values (in the reduce compute) to output -them to the screen. See the "Variable Accuracy" section of the -variable doc page for more details on insuring that -variables are current when they are evaluated between runs. -

    -

    The include style with its arg molecule adds atoms to a group that -have the same molecule ID as atoms already in the group. The molecule -ID = 0 is ignored in this operation, since it is assumed to flag -isolated atoms that are not part of molecules. An example of where -this operation is useful is if the region style has been used -previously to add atoms to a group that are within a geometric region. -If molecules straddle the region boundary, then atoms outside the -region that are part of molecules with atoms inside the region will -not be in the group. Using the group command a 2nd time with include -molecule will add those atoms that are outside the region to the -group. -

    -

    IMPORTANT NOTE: The include molecule operation is relatively -expensive in a parallel sense. This is because it requires -communication of relevant molecule IDs between all the processors and -each processor to loop over its atoms once per processor, to compare -its atoms to the list of molecule IDs from every other processor. -Hence it scales as N, rather than N/P as most of the group operations -do, where N is the number of atoms, and P is the number of processors. -

    -

    The subtract style takes a list of two or more existing group names -as arguments. All atoms that belong to the 1st group, but not to any -of the other groups are added to the specified group. -

    -

    The union style takes a list of one or more existing group names as -arguments. All atoms that belong to any of the listed groups are -added to the specified group. -

    -

    The intersect style takes a list of two or more existing group names -as arguments. Atoms that belong to every one of the listed groups are -added to the specified group. -

    -
    - -

    The dynamic style flags an existing or new group as dynamic. This -means atoms will be (re)assigned to the group periodically as a -simulation runs. This is in contrast to static groups where atoms are -permanently assigned to the group. The way the assignment occurs is -as follows. Only atoms in the group specified as the parent group via -the parent-ID are assigned to the dynamic group before the following -conditions are applied. If the region keyword is used, atoms not in -the specified region are removed from the dynamic group. If the var -keyword is used, the variable name must be an atom-style or -atomfile-style variable. The variable is evaluated and atoms whose -per-atom values are 0.0, are removed from the dynamic group. -

    -

    The assignment of atoms to a dynamic group is done at the beginning of -each run and on every timestep that is a multiple of N, which is the -argument for the every keyword (N = 1 is the default). For an -energy minimization, via the minimize command, an -assignement is made at the beginning of the minimization, but not -during the iterations of the minimizer. -

    -

    The point in the timestep at which atoms are assigned to a dynamic -group is after the initial stage of velocity Verlet time integration -has been performed, and before neighbor lists or forces are computed. -This is the point in the timestep where atom positions have just -changed due to the time integration, so the region criterion should be -accurate, if applied. -

    -

    IMPORTANT NOTE: If the region keyword is used to determine what -atoms are in the dynamic group, atoms can move outside of the -simulation box between reneighboring events. Thus if you want to -include all atoms on the left side of the simulation box, you probably -want to set the left boundary of the region to be outside the -simulation box by some reasonable amount (e.g. up to the cutoff of the -potential), else they may be excluded from the dynamic region. -

    -

    Here is an example of using a dynamic group to shrink the set of atoms -being integrated by using a spherical region with a variable radius -(shrinking from 18 to 5 over the course of the run). This could be -used to model a quench of the system, freezing atoms outside the -shrinking sphere, then converting the remaining atoms to a static -group and running further. -

    -
    variable        nsteps equal 5000
-variable        rad equal 18-(step/v_nsteps)*(18-5)
-region          ss sphere 20 20 0 v_rad
-group           mobile dynamic all region ss
-fix             1 mobile nve
-run             ${nsteps}
-group           mobile static
-run	        ${nsteps} 
-
    -

    IMPORTANT NOTE: All fixes and computes take a group ID as an argument, -but they do not all allow for use of a dynamic group. If you get an -error message that this is not allowed, but feel that it should be for -the fix or compute in question, then please post your reasoning to the -LAMMPS mail list and we can change it. -

    -

    The static style removes the setting for a dynamic group, converting -it to a static group (the default). The atoms in the static group are -those currently in the dynamic group. -

    -
    - -

    Restrictions: -

    -

    There can be no more than 32 groups defined at one time, including -"all". -

    -

    The parent group of a dynamic group cannot itself be a dynamic group. -

    -

    Related commands: -

    -

    dump, fix, region, -velocity -

    -

    Default: -

    -

    All atoms belong to the "all" group. -

    - diff --git a/doc/doc2/group2ndx.html b/doc/doc2/group2ndx.html deleted file mode 100644 index 3fb0670fcd..0000000000 --- a/doc/doc2/group2ndx.html +++ /dev/null @@ -1,58 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    group2ndx command -

    -

    Syntax: -

    -
    group2ndx file group-ID ... 
-
    -
    • file = name of index file to write out - -
    • zero or more group IDs may be appended - - -
    -

    Examples: -

    -
    group2ndx allindex.ndx
-group2ndx someindex.ndx upper lower mobile 
-
    -

    Description: -

    -

    Write a Gromacs style index file in text format that associates atom IDs -with the corresponding group definitions. This index file can be used -with in combination with Gromacs analysis tools or to import group -definitions into the fix colvars input file. -

    -

    Without specifying any group IDs, all groups will be written to the index -file. When specifying group IDs, only those groups will be written to the -index file. In order to follow the Gromacs conventions, the group all -will be renamed to System in the index file. -

    -
    - -

    Restrictions: -

    -

    This command requires that atoms have atom IDs, since this is the -information that is written to the index file. -

    -

    This fix is part of the USER-COLVARS package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    group, dump, fix colvars -

    -

    Default: none -

    - diff --git a/doc/doc2/if.html b/doc/doc2/if.html deleted file mode 100644 index ba4f5de6d4..0000000000 --- a/doc/doc2/if.html +++ /dev/null @@ -1,194 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    if command -

    -

    Syntax: -

    -
    if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ... 
-
    -
    • boolean = a Boolean expression evaluated as TRUE or FALSE (see below) -
    • then = required word -
    • t1,t2,...,tN = one or more LAMMPS commands to execute if condition is met, each enclosed in quotes -
    • elif = optional word, can appear multiple times -
    • f1,f2,...,fN = one or more LAMMPS commands to execute if elif condition is met, each enclosed in quotes (optional arguments) -
    • else = optional argument -
    • e1,e2,...,eN = one or more LAMMPS commands to execute if no condition is met, each enclosed in quotes (optional arguments) -
    -

    Examples: -

    -
    if "${steps} > 1000" then quit
-if "${myString} == a10" then quit
-if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
-if "(${eng} > 0.0) || ($n < 1000)" then &
-  "timestep 0.005" &
-elif $n<10000 &
-  "timestep 0.01" &
-else &
-  "timestep 0.02" &
-  "print 'Max step reached'"
-if "${eng} > ${eng_previous}" then "jump file1" else "jump file2" 
-
    -

    Description: -

    -

    This command provides an if-then-else capability within an input -script. A Boolean expression is evaluted and the result is TRUE or -FALSE. Note that as in the examples above, the expression can contain -variables, as defined by the variable command, which -will be evaluated as part of the expression. Thus a user-defined -formula that reflects the current state of the simulation can be used -to issue one or more new commands. -

    -

    If the result of the Boolean expression is TRUE, then one or more -commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean -expressions associated with successive elif keywords are evaluated -until one is found to be true, in which case its commands (f1, f2, -..., fN) are executed. If no Boolean expression is TRUE, then the -commands associated with the else keyword, namely (e1, e2, ..., eN), -are executed. The elif and else keywords and their associated -commands are optional. If they aren't specified and the initial -Boolean expression is FALSE, then no commands are executed. -

    -

    The syntax for Boolean expressions is described below. -

    -

    Each command (t1, f1, e1, etc) can be any valid LAMMPS input script -command, except an include command, which is not -allowed. If the command is more than one word, it must enclosed in -quotes, so it will be treated as a single argument, as in the examples -above. -

    -

    IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a -print command), then double and single quotes can be used -and nested in the usual manner, as in the examples above and below. -See Section_commands 2 of the manual for -more details on using quotes in arguments. Only one of level of -nesting is allowed, but that should be sufficient for most use cases. -

    -

    Note that by using the line continuation character "&", the if command -can be spread across many lines, though it is still a single command: -

    -
    if "$a < $b" then &
-  "print 'Minimum value = $a'" &
-  "run 1000" &
-else &      
-  'print "Minimum value = $b"' &
-  "minimize 0.001 0.001 1000 10000" 
-
    -

    Note that if one of the commands to execute is quit, as in -the first example above, then executing the command will cause LAMMPS -to halt. -

    -

    Note that by jumping to a label in the same input script, the if -command can be used to break out of a loop. See the variable -delete command for info on how to delete the associated -loop variable, so that it can be re-used later in the input script. -

    -

    Here is an example of a loop which checks every 1000 steps if the -system temperature has reached a certain value, and if so, breaks out -of the loop to finish the run. Note that any variable could be -checked, so long as it is current on the timestep when the run -completes. As explained on the variable doc page, -this can be insured by includig the variable in thermodynamic output. -

    -
    variable myTemp equal temp
-label loop
-variable a loop 1000
-run 1000
-if "${myTemp} < 300.0" then "jump SELF break"
-next a
-jump SELF loop
-label break
-print "ALL DONE" 
-
    -

    Here is an example of a double loop which uses the if and -jump commands to break out of the inner loop when a -condition is met, then continues iterating thru the outer loop. -

    -
    label	    loopa
-variable    a loop 5
-  label	    loopb
-  variable  b loop 5
-  print	    "A,B = $a,$b"
-  run       10000
-  if	    "$b > 2" then "jump SELF break"
-  next	    b
-  jump	    in.script loopb
-label	    break
-variable    b delete
-next	    a
-jump	    SELF loopa 
-
    -
    - -

    The Boolean expressions for the if and elif keywords have a C-like -syntax. Note that each expression is a single argument within the if -command. Thus if you want to include spaces in the expression for -clarity, you must enclose the entire expression in quotes. -

    -

    An expression is built out of numbers (which start with a digit or -period or minus sign) or strings (which start with a letter and can -contain alphanumeric characters or underscores): -

    -
    0.2, 100, 1.0e20, -15.4, etc 
-InP, myString, a123, ab_23_cd, etc 
-
    -

    and Boolean operators: -

    -
    A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A || B, !A 
-
    -

    Each A and B is a number or string or a variable reference like $a or -${abc}, or A or B can be another Boolean expression. -

    -

    If a variable is used it can produce a number when evaluated, like an -equal-style variable. Or it can produce a string, -like an index-style variable. For an individual -Boolean operator, A and B must both be numbers or must both be -strings. You cannot compare a number to a string. -

    -

    Expressions are evaluated left to right and have the usual C-style -precedence: the unary logical NOT operator "!" has the highest -precedence, the 4 relational operators "<", "<=", ">", and ">=" are -next; the two remaining relational operators "==" and "!=" are next; -then the logical AND operator "&&"; and finally the logical OR -operator "||" has the lowest precedence. Parenthesis can be used to -group one or more portions of an expression and/or enforce a different -order of evaluation than what would occur with the default precedence. -

    -

    When the 6 relational operators (first 6 in list above) compare 2 -numbers, they return either a 1.0 or 0.0 depending on whether the -relationship between A and B is TRUE or FALSE. When the 6 relational -operators compare 2 strings, they also return a 1.0 or 0.0 for TRUE or -FALSE, but the comparison is done by the C function strcmp(). -

    -

    When the 3 logical operators (last 3 in list above) compare 2 numbers, -they also return either a 1.0 or 0.0 depending on whether the -relationship between A and B is TRUE or FALSE (or just A). The -logical AND operator will return 1.0 if both its arguments are -non-zero, else it returns 0.0. The logical OR operator will return -1.0 if either of its arguments is non-zero, else it returns 0.0. The -logical NOT operator returns 1.0 if its argument is 0.0, else it -returns 0.0. The 3 logical operators can only be used to operate on -numbers, not on strings. -

    -

    The overall Boolean expression produces a TRUE result if the result is -non-zero. If the result is zero, the expression result is FALSE. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    variable, print -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_class2.html b/doc/doc2/improper_class2.html deleted file mode 100644 index da32179c3d..0000000000 --- a/doc/doc2/improper_class2.html +++ /dev/null @@ -1,131 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style class2 command -

    -

    improper_style class2/omp command -

    -

    Syntax: -

    -
    improper_style class2 
-
    -

    Examples: -

    -
    improper_style class2
-improper_coeff 1 100.0 0
-improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 
-
    -

    Description: -

    -

    The class2 improper style uses the potential -

    -
    -
    -

    where Ei is the improper term and Eaa is an angle-angle term. The 3 X -terms in Ei are an average over 3 out-of-plane angles. -

    -

    The 4 atoms in an improper quadruplet (listed in the data file read by -the read_data command) are ordered I,J,K,L. X_IJKL -refers to the angle between the plane of I,J,K and the plane of J,K,L, -and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK. -Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X -terms. Thus J (the 2nd atom in the quadruplet) is the atom of -symmetry in the 3 X angles. -

    -

    The subscripts on the various theta's refer to different combinations -of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL -is the angle formed by atoms I,J,L with J in the middle. Theta1, -theta2, theta3 are the equilibrium positions of those angles. Again, -atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the -theta angles, since it is always the center atom. -

    -

    Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L -would exist for an improper to be defined between the 4 atoms, but -this is not required. -

    -

    See (Sun) for a description of the COMPASS class2 force field. -

    -

    Coefficients for the Ei and Eaa formulas must be defined for each -improper type via the improper_coeff command as -in the example above, or in the data file or restart files read by the -read_data or read_restart -commands. -

    -

    These are the 2 coefficients for the Ei formula: -

    -
    • K (energy/radian^2) -
    • X0 (degrees) -
    -

    X0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

    -

    For the Eaa formula, each line in a -improper_coeff command in the input script lists -7 coefficients, the first of which is "aa" to indicate they are -AngleAngle coefficients. In a data file, these coefficients should be -listed under a "AngleAngle Coeffs" heading and you must leave out the -"aa", i.e. only list 6 coefficients after the improper type. -

    -
    • aa -
    • M1 (energy/distance) -
    • M2 (energy/distance) -
    • M3 (energy/distance) -
    • theta1 (degrees) -
    • theta2 (degrees) -
    • theta3 (degrees) -
    -

    The theta values are specified in degrees, but LAMMPS converts them to -radians internally; hence the units of M are in energy/radian^2. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This improper style can only be used if LAMMPS was built with the -CLASS2 package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: none -

    -
    - - - -

    (Sun) Sun, J Phys Chem B 102, 7338-7364 (1998). -

    - diff --git a/doc/doc2/improper_coeff.html b/doc/doc2/improper_coeff.html deleted file mode 100644 index bd67c5f64d..0000000000 --- a/doc/doc2/improper_coeff.html +++ /dev/null @@ -1,102 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_coeff command -

    -

    Syntax: -

    -
    improper_coeff N args 
-
    -
    • N = improper type (see asterisk form below) -
    • args = coefficients for one or more improper types -
    -

    Examples: -

    -
    improper_coeff 1 300.0 0.0
-improper_coeff * 80.2 -1 2
-improper_coeff *4 80.2 -1 2 
-
    -

    Description: -

    -

    Specify the improper force field coefficients for one or more improper -types. The number and meaning of the coefficients depends on the -improper style. Improper coefficients can also be set in the data -file read by the read_data command or in a restart -file. -

    -

    N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple improper types. This takes -the form "*" or "*n" or "n*" or "m*n". If N = the number of improper -types, then an asterisk with no numeric values means all types from 1 -to N. A leading asterisk means all types from 1 to n (inclusive). A -trailing asterisk means all types from n to N (inclusive). A middle -asterisk means all types from m to n (inclusive). -

    -

    Note that using an improper_coeff command can override a previous -setting for the same improper type. For example, these commands set -the coeffs for all improper types, then overwrite the coeffs for just -improper type 2: -

    -
    improper_coeff * 300.0 0.0
-improper_coeff 2 50.0 0.0 
-
    -

    A line in a data file that specifies improper coefficients uses the -exact same format as the arguments of the improper_coeff command in an -input script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Improper Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as -

    -
    1 300.0 0.0 
-
    -

    The improper_style class2 is an exception to -this rule, in that an additional argument is used in the input script -to allow specification of the cross-term coefficients. See its doc -page for details. -

    -
    - -

    Here is an alphabetic list of improper styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated improper_coeff command. -

    -

    Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -this page. -

    - - -
    - -

    Restrictions: -

    -

    This command must come after the simulation box is defined by a -read_data, read_restart, or -create_box command. -

    -

    An improper style must be defined before any improper coefficients are -set, either in the input script or in a data file. -

    -

    Related commands: -

    -

    improper_style -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_cossq.html b/doc/doc2/improper_cossq.html deleted file mode 100644 index 6bdb36927c..0000000000 --- a/doc/doc2/improper_cossq.html +++ /dev/null @@ -1,95 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style cossq command -

    -

    improper_style cossq/omp command -

    -

    Syntax: -

    -
    improper_style cossq 
-
    -

    Examples: -

    -
    improper_style cossq
-improper_coeff 1 4.0 0.0 
-
    -

    Description: -

    -

    The cossq improper style uses the potential -

    -
    -
    -

    where x is the improper angle, x0 is its equilibrium value, and K is a -prefactor. -

    -

    If the 4 atoms in an improper quadruplet (listed in the data file read -by the read_data command) are ordered I,J,K,L then X -is the angle between the plane of I,J,K and the plane of J,K,L. -Alternatively, you can think of atoms J,K,L as being in a plane, and -atom I above the plane, and X as a measure of how far out-of-plane I -is with respect to the other 3 atoms. -

    -

    Note that defining 4 atoms to interact in this way, does not mean that -bonds necessarily exist between I-J, J-K, or K-L, as they would in a -linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an -improper to be defined between the 4 atoms. -

    -

    The following coefficients must be defined for each improper type via -the improper_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • K (energy/radian^2) -
    • X0 (degrees) -
    -

    X0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_cvff.html b/doc/doc2/improper_cvff.html deleted file mode 100644 index b437e7c029..0000000000 --- a/doc/doc2/improper_cvff.html +++ /dev/null @@ -1,92 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style cvff command -

    -

    improper_style cvff/omp command -

    -

    Syntax: -

    -
    improper_style cvff 
-
    -

    Examples: -

    -
    improper_style cvff
-improper_coeff 1 80.0 -1 4 
-
    -

    Description: -

    -

    The cvff improper style uses the potential -

    -
    -
    -

    where phi is the improper dihedral angle. -

    -

    If the 4 atoms in an improper quadruplet (listed in the data file read -by the read_data command) are ordered I,J,K,L then -the improper dihedral angle is between the plane of I,J,K and the -plane of J,K,L. Note that because this is effectively a dihedral -angle, the formula for this improper style is the same as for -dihedral_style harmonic. -

    -

    Note that defining 4 atoms to interact in this way, does not mean that -bonds necessarily exist between I-J, J-K, or K-L, as they would in a -linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an -improper to be defined between the 4 atoms. -

    -

    The following coefficients must be defined for each improper type via -the improper_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • K (energy) -
    • d (+1 or -1) -
    • n (0,1,2,3,4,6) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This improper style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_fourier.html b/doc/doc2/improper_fourier.html deleted file mode 100644 index 5b3478deb5..0000000000 --- a/doc/doc2/improper_fourier.html +++ /dev/null @@ -1,87 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style fourier command -

    -

    improper_style fourier/omp command -

    -

    Syntax: -

    -
    improper_style fourier 
-
    -

    Examples: -

    -
    improper_style fourier
-improper_coeff 1 100.0 180.0 
-
    -

    Description: -

    -

    The fourier improper style uses the following potential: -

    -
    -
    -

    where K is the force constant and omega is the angle between the IL -axis and the IJK plane: -

    -
    -
    -

    If all parameter (see bellow) is not zero, the all the three possible angles will taken in account. -

    -

    The following coefficients must be defined for each improper type via -the improper_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • K (energy) -
    • C0 (real) -
    • C1 (real) -
    • C2 (real) -
    • all (integer >= 0) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_harmonic.html b/doc/doc2/improper_harmonic.html deleted file mode 100644 index 771d27faaa..0000000000 --- a/doc/doc2/improper_harmonic.html +++ /dev/null @@ -1,97 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style harmonic command -

    -

    improper_style harmonic/kk command -

    -

    improper_style harmonic/omp command -

    -

    Syntax: -

    -
    improper_style harmonic 
-
    -

    Examples: -

    -
    improper_style harmonic
-improper_coeff 1 100.0 0 
-
    -

    Description: -

    -

    The harmonic improper style uses the potential -

    -
    -
    -

    where X is the improper angle, X0 is its equilibrium value, and K is a -prefactor. Note that the usual 1/2 factor is included in K. -

    -

    If the 4 atoms in an improper quadruplet (listed in the data file read -by the read_data command) are ordered I,J,K,L then X -is the angle between the plane of I,J,K and the plane of J,K,L. -Alternatively, you can think of atoms J,K,L as being in a plane, and -atom I above the plane, and X as a measure of how far out-of-plane I -is with respect to the other 3 atoms. -

    -

    Note that defining 4 atoms to interact in this way, does not mean that -bonds necessarily exist between I-J, J-K, or K-L, as they would in a -linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an -improper to be defined between the 4 atoms. -

    -

    The following coefficients must be defined for each improper type via -the improper_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • K (energy/radian^2) -
    • X0 (degrees) -
    -

    X0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This improper style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_hybrid.html b/doc/doc2/improper_hybrid.html deleted file mode 100644 index c0903b607f..0000000000 --- a/doc/doc2/improper_hybrid.html +++ /dev/null @@ -1,75 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style hybrid command -

    -

    Syntax: -

    -
    improper_style hybrid style1 style2 ... 
-
    -
    • style1,style2 = list of one or more improper styles -
    -

    Examples: -

    -
    improper_style hybrid harmonic helix
-improper_coeff 1 harmonic 120.0 30
-improper_coeff 2 cvff 20.0 -1 2 
-
    -

    Description: -

    -

    The hybrid style enables the use of multiple improper styles in one -simulation. An improper style is assigned to each improper type. For -example, impropers in a polymer flow (of improper type 1) could be -computed with a harmonic potential and impropers in the wall -boundary (of improper type 2) could be computed with a cvff -potential. The assignment of improper type to style is made via the -improper_coeff command or in the data file. -

    -

    In the improper_coeff command, the first coefficient sets the improper -style and the remaining coefficients are those appropriate to that -style. In the example above, the 2 improper_coeff commands would set -impropers of improper type 1 to be computed with a harmonic -potential with coefficients 120.0, 30 for K, X0. Improper type 2 -would be computed with a cvff potential with coefficients 20.0, -1, -2 for K, d, n. -

    -

    If the improper class2 potential is one of the hybrid styles, it -requires additional AngleAngle coefficients be specified in the data -file. These lines must also have an additional "class2" argument -added after the improper type. For improper types which are assigned -to other hybrid styles, use the style name (e.g. "harmonic") -appropriate to that style. The AngleAngle coeffs for that improper -type will then be ignored. -

    -

    An improper style of none can be specified as the 2nd argument to -the improper_coeff command, if you desire to turn off certain improper -types. -

    -
    - -

    Restrictions: -

    -

    This improper style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Unlike other improper styles, the hybrid improper style does not store -improper coefficient info for individual sub-styles in a binary -restart files. Thus when retarting a simulation from a -restart file, you need to re-specify improper_coeff commands. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_none.html b/doc/doc2/improper_none.html deleted file mode 100644 index bfd664f385..0000000000 --- a/doc/doc2/improper_none.html +++ /dev/null @@ -1,34 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style none command -

    -

    Syntax: -

    -
    improper_style none 
-
    -

    Examples: -

    -
    improper_style none 
-
    -

    Description: -

    -

    Using an improper style of none means improper forces are not -computed, even if quadruplets of improper atoms were listed in the -data file read by the read_data command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/improper_ring.html b/doc/doc2/improper_ring.html deleted file mode 100644 index 9e1ab3c26a..0000000000 --- a/doc/doc2/improper_ring.html +++ /dev/null @@ -1,102 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style ring command -

    -

    improper_style ring/omp command -

    -

    Syntax: -

    -
    improper_style ring 
-
    -

    Examples: -

    -
    improper_style ring
-improper_coeff 1 8000 70.5 
-
    -

    Description: -

    -

    The ring improper style uses the potential -

    -
    -
    -

    where K is a prefactor, theta is the angle formed by the atoms -specified by (i,j,k,l) indices and theta0 its equilibrium value. -

    -

    If the 4 atoms in an improper quadruplet (listed in the data file read -by the read_data command) are ordered i,j,k,l then -theta_ijl is the angle between atoms i,j and l, theta_ijk is the -angle between atoms i,j and k, theta_kjl is the angle between atoms -j,k, and l. -

    -

    The "ring" improper style implements the improper potential introduced -by Destree et al., in Equation (9) of (Destree). This -potential does not affect small amplitude vibrations but is used in an -ad-hoc way to prevent the onset of accidentially large amplitude -fluctuations leading to the occurrence of a planar conformation of the -three bonds i-j, j-k and j-l, an intermediate conformation toward the -chiral inversion of a methine carbon. In the "Impropers" section of -data file four atoms: i, j, k and l are specified with i,j and l lying -on the backbone of the chain and k specifying the chirality of j. -

    -

    The following coefficients must be defined for each improper type via -the improper_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • K (energy/radian^2) -
    • theta0 (degrees) -
    -

    theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    Related commands: -

    -

    improper_coeff -

    - - -

    (Destree) M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, -J Chem Phys, 112, 9632 (2000). -

    - diff --git a/doc/doc2/improper_style.html b/doc/doc2/improper_style.html deleted file mode 100644 index c7deed3da6..0000000000 --- a/doc/doc2/improper_style.html +++ /dev/null @@ -1,99 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style command -

    -

    Syntax: -

    -
    improper_style style 
-
    -
    • style = none or hybrid or class2 or cvff or harmonic -
    -

    Examples: -

    -
    improper_style harmonic
-improper_style cvff
-improper_style hybrid cvff harmonic 
-
    -

    Description: -

    -

    Set the formula(s) LAMMPS uses to compute improper interactions -between quadruplets of atoms, which remain in force for the duration -of the simulation. The list of improper quadruplets is read in by a -read_data or read_restart command -from a data or restart file. Note that the ordering of the 4 atoms in -an improper quadruplet determines the the definition of the improper -angle used in the formula for each style. See the doc pages of -individual styles for details. -

    -

    Hybrid models where impropers are computed using different improper -potentials can be setup using the hybrid improper style. -

    -

    The coefficients associated with an improper style can be specified in -a data or restart file or via the improper_coeff -command. -

    -

    All improper potentials store their coefficient data in binary restart -files which means improper_style and -improper_coeff commands do not need to be -re-specified in an input script that restarts a simulation. See the -read_restart command for details on how to do -this. The one exception is that improper_style hybrid only stores -the list of sub-styles in the restart file; improper coefficients need -to be re-specified. -

    -

    IMPORTANT NOTE: When both an improper and pair style is defined, the -special_bonds command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between a group of 4 bonded atoms. -

    -
    - -

    Here is an alphabetic list of improper styles defined in LAMMPS. -Click on the style to display the formula it computes and coefficients -specified by the associated improper_coeff -command. -

    -

    Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -this page. -

    - - -
    - -

    Restrictions: -

    -

    Improper styles can only be set for atom_style choices that allow -impropers to be defined. -

    -

    Most improper styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info on packages. -The doc pages for individual improper potentials tell if it is part of -a package. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: -

    -
    improper_style none 
-
    - diff --git a/doc/doc2/improper_umbrella.html b/doc/doc2/improper_umbrella.html deleted file mode 100644 index 2774452ae0..0000000000 --- a/doc/doc2/improper_umbrella.html +++ /dev/null @@ -1,97 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    improper_style umbrella command -

    -

    improper_style umbrella/omp command -

    -

    Syntax: -

    -
    improper_style umbrella 
-
    -

    Examples: -

    -
    improper_style umbrella
-improper_coeff 1 100.0 180.0 
-
    -

    Description: -

    -

    The umbrella improper style uses the following potential, which is -commonly referred to as a classic inversion and used in the -DREIDING force field: -

    -
    -
    -

    where K is the force constant and omega is the angle between the IL -axis and the IJK plane: -

    -
    -
    -

    If omega0 = 0 the potential term has a minimum for the planar -structure. Otherwise it has two minima at +/- omega0, with a barrier -in between. -

    -

    See (Mayo) for a description of the DREIDING force field. -

    -

    The following coefficients must be defined for each improper type via -the improper_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • K (energy) -
    • omega0 (degrees) -
    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This improper style can only be used if LAMMPS was built with the -MOLECULE package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    improper_coeff -

    -

    Default: none -

    -
    - - - -

    (Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990), -

    - diff --git a/doc/doc2/include.html b/doc/doc2/include.html deleted file mode 100644 index f7ba914eac..0000000000 --- a/doc/doc2/include.html +++ /dev/null @@ -1,45 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    include command -

    -

    Syntax: -

    -
    include file 
-
    -
    • file = filename of new input script to switch to -
    -

    Examples: -

    -
    include newfile
-include in.run2 
-
    -

    Description: -

    -

    This command opens a new input script file and begins reading LAMMPS -commands from that file. When the new file is finished, the original -file is returned to. Include files can be nested as deeply as -desired. If input script A includes script B, and B includes A, then -LAMMPS could run for a long time. -

    -

    If the filename is a variable (see the variable -command), different processor partitions can run different input -scripts. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    variable, jump -

    -

    Default: none -

    - diff --git a/doc/doc2/info.html b/doc/doc2/info.html deleted file mode 100644 index 36a7d4baf4..0000000000 --- a/doc/doc2/info.html +++ /dev/null @@ -1,91 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    info command -

    -

    Syntax: -

    -
    info args 
-
    -

    args = one or more of the following keywords: out, all, system, communication, computes, dumps, fixes, groups, regions, variables, time, or configuration - out values = screen, log, append filename, overwrite filename:ul -

    -

    Examples: -

    -
    info system
-info groups computes variables
-info all out log
-info all out append info.txt 
-
    -

    Description: -

    -

    Print out information about the current internal state of the running -LAMMPS process. This can be helpful when debugging or validating -complex input scripts. Several output categories are available and -one or more output category may be requested. -

    -

    The out flag controls where the output is sent. It can only be sent -to one target. By default this is the screen, if it is active. The -log argument selects the log file instead. With the append and -overwrite option, followed by a filename, the output is written -to that file, which is either appended to or overwritten, respectively. -

    -

    The all flag activates printing all categories listed below. -

    -

    The system category prints a general system overview listing. This -includes the unit style, atom style, number of atoms, bonds, angles, -dihedrals, and impropers and the number of the respective types, box -dimensions and properties, force computing styles and more. -

    -

    The communication category prints a variety of information about -communication and parallelization: the MPI library version level, -the number of MPI ranks and OpenMP threads, the communication style -and layout, the processor grid dimensions, ghost atom communication -mode, cutoff, and related settings. -

    -

    The computes category prints a list of all currently defined -computes, their IDs and styles and groups they operate on. -

    -

    The dumps category prints a list of all currently active dumps, -their IDs, styles, filenames, groups, and dump frequencies. -

    -

    The fixes category prints a list of all currently defined fixes, -their IDs and styles and groups they operate on. -

    -

    The groups category prints a list of all currently defined groups. -

    -

    The regions category prints a list of all currently defined regions, -their IDs and styles and whether "inside" or "outside" atoms are -selected. -

    -

    The variables category prints a list of all currently defined -variables, their names, styles, definition and last computed value, if -available. -

    -

    The time category prints the accumulated CPU and wall time for the -process that writes output (usually MPI rank 0). -

    -

    The configuration command prints some information about the LAMMPS -version and architection and OS it is run on. Where supported, also -information about the memory consumption provided by the OS is -reported. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    print -

    -

    Default: -

    -

    The out option has the default screen. -

    - diff --git a/doc/doc2/jump.html b/doc/doc2/jump.html deleted file mode 100644 index 5fa7246628..0000000000 --- a/doc/doc2/jump.html +++ /dev/null @@ -1,136 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    jump command -

    -

    Syntax: -

    -
    jump file label 
-
    -
    • file = filename of new input script to switch to -
    • label = optional label within file to jump to -
    -

    Examples: -

    -
    jump newfile
-jump in.run2 runloop
-jump SELF runloop 
-
    -

    Description: -

    -

    This command closes the current input script file, opens the file with -the specified name, and begins reading LAMMPS commands from that file. -Unlike the include command, the original file is not -returned to, although by using multiple jump commands it is possible -to chain from file to file or back to the original file. -

    -

    If the word "SELF" is used for the filename, then the current input -script is re-opened and read again. -

    -

    IMPORTANT NOTE: The SELF option is not guaranteed to work when the -current input script is being read through stdin (standard input), -e.g. -

    -
    lmp_g++ < in.script 
-
    -

    since the SELF option invokes the C-library rewind() call, which may -not be supported for stdin on some systems or by some MPI -implementations. This can be worked around by using the -in -command-line argument, e.g. -

    -
    lmp_g++ -in in.script 
-
    -

    or by using the -var command-line -argument to pass the script name as a -variable to the input script. In the latter case, a -variable called "fname" could be used in place of -SELF, e.g. -

    -
    lmp_g++ -var fname in.script < in.script 
-
    -

    The 2nd argument to the jump command is optional. If specified, it is -treated as a label and the new file is scanned (without executing -commands) until the label is found, and commands are executed from -that point forward. This can be used to loop over a portion of the -input script, as in this example. These commands perform 10 runs, -each of 10000 steps, and create 10 dump files named file.1, file.2, -etc. The next command is used to exit the loop after 10 -iterations. When the "a" variable has been incremented for the tenth -time, it will cause the next jump command to be skipped. -

    -
    variable a loop 10
-label loop
-dump 1 all atom 100 file.$a
-run 10000
-undump 1
-next a
-jump in.lj loop 
-
    -

    If the jump file argument is a variable, the jump command can be -used to cause different processor partitions to run different input -scripts. In this example, LAMMPS is run on 40 processors, with 4 -partitions of 10 procs each. An in.file containing the example -variable and jump command will cause each partition to run a different -simulation. -

    -
    mpirun -np 40 lmp_ibm -partition 4x10 -in in.file 
-
    -
    variable f world script.1 script.2 script.3 script.4
-jump $f 
-
    -

    Here is an example of a loop which checks every 1000 steps if the -system temperature has reached a certain value, and if so, breaks out -of the loop to finish the run. Note that any variable could be -checked, so long as it is current on the timestep when the run -completes. As explained on the variable doc page, -this can be insured by includig the variable in thermodynamic output. -

    -
    variable myTemp equal temp
-label loop
-variable a loop 1000
-run 1000
-if "${myTemp} < 300.0" then "jump SELF break"
-next a
-jump SELF loop
-label break
-print "ALL DONE" 
-
    -

    Here is an example of a double loop which uses the if and -jump commands to break out of the inner loop when a -condition is met, then continues iterating thru the outer loop. -

    -
    label	    loopa
-variable    a loop 5
-  label	    loopb
-  variable  b loop 5
-  print	    "A,B = $a,$b"
-  run       10000
-  if	    "$b > 2" then "jump SELF break"
-  next	    b
-  jump	    in.script loopb
-label	    break
-variable    b delete
-next	    a
-jump	    SELF loopa 
-
    -

    Restrictions: -

    -

    If you jump to a file and it does not contain the specified label, -LAMMPS will come to the end of the file and exit. -

    -

    Related commands: -

    -

    variable, include, label, -next -

    -

    Default: none -

    - diff --git a/doc/doc2/kspace_modify.html b/doc/doc2/kspace_modify.html deleted file mode 100644 index 25693a130d..0000000000 --- a/doc/doc2/kspace_modify.html +++ /dev/null @@ -1,350 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    kspace_modify command -

    -

    Syntax: -

    -
    kspace_modify keyword value ... 
-
    -
    • one or more keyword/value pairs may be listed - -
      keyword = mesh or order or order/disp or mix/disp or overlap or minorder or force or gewald or gewald/disp or slab or (nozforce or compute or cutoff/adjust or fftbench or collective or diff or kmax/ewald or force/disp/real or force/disp/kspace or splittol or disp/auto:l
-  mesh value = x y z
-    x,y,z = grid size in each dimension for long-range Coulombics
-  mesh/disp value = x y z
-    x,y,z = grid size in each dimension for 1/r^6 dispersion
-  order value = N
-    N = extent of Gaussian for PPPM or MSM mapping of charge to grid
-  order/disp value = N
-    N = extent of Gaussian for PPPM mapping of dispersion term to grid
-  mix/disp value = pair or geom or none
-  overlap = yes or no = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
-  minorder value = M
-    M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
-  force value = accuracy (force units)
-  gewald value = rinv (1/distance units)
-    rinv = G-ewald parameter for Coulombics
-  gewald/disp value = rinv (1/distance units)
-    rinv = G-ewald parameter for dispersion
-  slab value = volfactor or nozforce
-    volfactor = ratio of the total extended volume used in the
-      2d approximation compared with the volume of the simulation domain
-  nozforce turns off kspace forces in the z direction
-  compute value = yes or no 
-  cutoff/adjust value = yes or no 
-  pressure/scalar value = yes or no 
-  fftbench value = yes or no 
-  collective value = yes or no 
-  diff value = ad or ik = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode 
-  kmax/ewald value = kx ky kz 
-    kx,ky,kz = number of Ewald sum kspace vectors in each dimension
-  force/disp/real value = accuracy (force units)
-  force/disp/kspace value = accuracy (force units)
-  splittol value = tol
-    tol = relative size of two eigenvalues (see discussion below)
-  disp/auto value = yes or no 
-
      - -
    -

    Examples: -

    -
    kspace_modify mesh 24 24 30 order 6
-kspace_modify slab 3.0 
-
    -

    Description: -

    -

    Set parameters used by the kspace solvers defined by the -kspace_style command. Not all parameters are -relevant to all kspace styles. -

    -

    The mesh keyword sets the grid size for kspace style pppm or -msm. In the case of PPPM, this is the FFT mesh, and each dimension -must be factorizable into powers of 2, 3, and 5. In the case of MSM, -this is the finest scale real-space mesh, and each dimension must be -factorizable into powers of 2. When this option is not set, the PPPM -or MSM solver chooses its own grid size, consistent with the -user-specified accuracy and pairwise cutoff. Values for x,y,z of -0,0,0 unset the option. -

    -

    The mesh/disp keyword sets the grid size for kspace style -pppm/disp. This is the FFT mesh for long-range dispersion and ach -dimension must be factorizable into powers of 2, 3, and 5. When this -option is not set, the PPPM solver chooses its own grid size, -consistent with the user-specified accuracy and pairwise cutoff. -Values for x,y,z of 0,0,0 unset the option. -

    -

    The order keyword determines how many grid spacings an atom's charge -extends when it is mapped to the grid in kspace style pppm or msm. -The default for this parameter is 5 for PPPM and 8 for MSM, which -means each charge spans 5 or 8 grid cells in each dimension, -respectively. For the LAMMPS implementation of MSM, the order can -range from 4 to 10 and must be even. For PPPM, the minimum allowed -setting is 2 and the maximum allowed setting is 7. The larger the -value of this parameter, the smaller that LAMMPS will set the grid -size, to achieve the requested accuracy. Conversely, the smaller the -order value, the larger the grid size will be. Note that there is an -inherent trade-off involved: a small grid will lower the cost of FFTs -or MSM direct sum, but a larger order parameter will increase the cost -of interpolating charge/fields to/from the grid. -

    -

    The order/disp keyword determines how many grid spacings an atom's -dispersion term extends when it is mapped to the grid in kspace style -pppm/disp. It has the same meaning as the order setting for -Coulombics. -

    -

    The overlap keyword can be used in conjunction with the minorder -keyword with the PPPM styles to adjust the amount of communication -that occurs when values on the FFT grid are exchangeed between -processors. This communication is distinct from the communication -inherent in the parallel FFTs themselves, and is required because -processors interpolate charge and field values using grid point values -owned by neighboring processors (i.e. ghost point communication). If -the overlap keyword is set to yes then this communication is -allowed to extend beyond nearest-neighbor processors, e.g. when using -lots of processors on a small problem. If it is set to no then the -communication will be limited to nearest-neighbor processors and the -order setting will be reduced if necessary, as explained by the -minorder keyword discussion. The overlap keyword is always set to -yes in MSM. -

    -

    The minorder keyword allows LAMMPS to reduce the order setting if -necessary to keep the communication of ghost grid point limited to -exchanges between nearest-neighbor processors. See the discussion of -the overlap keyword for details. If the overlap keyword is set to -yes, which is the default, this is never needed. If it set to no -and overlap occurs, then LAMMPS will reduce the order setting, one -step at a time, until the ghost grid overlap only extends to nearest -neighbor processors. The minorder keyword limits how small the -order setting can become. The minimum allowed value for PPPM is 2, -which is the default. If minorder is set to the same value as -order then no reduction is allowed, and LAMMPS will generate an -error if the grid communcation is non-nearest-neighbor and overlap -is set to no. The minorder keyword is not currently supported in -MSM. -

    -

    The PPPM order parameter may be reset by LAMMPS when it sets up the -FFT grid if the implied grid stencil extends beyond the grid cells -owned by neighboring processors. Typically this will only occur when -small problems are run on large numbers of processors. A warning will -be generated indicating the order parameter is being reduced to allow -LAMMPS to run the problem. Automatic adjustment of the order parameter -is not supported in MSM. -

    -

    The force keyword overrides the relative accuracy parameter set by -the kspace_style command with an absolute -accuracy. The accuracy determines the RMS error in per-atom forces -calculated by the long-range solver and is thus specified in force -units. A negative value for the accuracy setting means to use the -relative accuracy parameter. The accuracy setting is used in -conjunction with the pairwise cutoff to determine the number of -K-space vectors for style ewald, the FFT grid size for style -pppm, or the real space grid size for style msm. -

    -

    The gewald keyword sets the value of the Ewald or PPPM G-ewald -parameter for charge as rinv in reciprocal distance units. Without -this setting, LAMMPS chooses the parameter automatically as a function -of cutoff, precision, grid spacing, etc. This means it can vary from -one simulation to the next which may not be desirable for matching a -KSpace solver to a pre-tabulated pairwise potential. This setting can -also be useful if Ewald or PPPM fails to choose a good grid spacing -and G-ewald parameter automatically. If the value is set to 0.0, -LAMMPS will choose the G-ewald parameter automatically. MSM does not -use the gewald parameter. -

    -

    The gewald/disp keyword sets the value of the Ewald or PPPM G-ewald -parameter for dispersion as rinv in reciprocal distance units. It -has the same meaning as the gewald setting for Coulombics. -

    -

    The slab keyword allows an Ewald or PPPM solver to be used for a -systems that are periodic in x,y but non-periodic in z - a -boundary setting of "boundary p p f". This is done by -treating the system as if it were periodic in z, but inserting empty -volume between atom slabs and removing dipole inter-slab interactions -so that slab-slab interactions are effectively turned off. The -volfactor value sets the ratio of the extended dimension in z divided -by the actual dimension in z. The recommended value is 3.0. A larger -value is inefficient; a smaller value introduces unwanted slab-slab -interactions. The use of fixed boundaries in z means that the user -must prevent particle migration beyond the initial z-bounds, typically -by providing a wall-style fix. The methodology behind the slab -option is explained in the paper by (Yeh). The slab option -is also extended to non-neutral systems -(Ballenegger). An alternative slab option can be -invoked with the nozforce keyword in lieu of the volfactor. This -turns off all kspace forces in the z direction. The nozforce option -is not supported by MSM. For MSM, any combination of periodic, -non-periodic, or shrink-wrapped boundaries can be set using -boundary (the slab approximation in not needed). The -slab keyword is not currently supported by Ewald or PPPM when using -a triclinic simulation cell. The slab correction has also been -extended to point dipole interactions (Klapp) in -kspace_style ewald/disp. -

    -

    The compute keyword allows Kspace computations to be turned off, -even though a kspace_style is defined. This is -not useful for running a real simulation, but can be useful for -debugging purposes or for computing only partial forces that do not -include the Kspace contribution. You can also do this by simply not -defining a kspace_style, but a Kspace-compatible -pair_style requires a kspace style to be defined. -This keyword gives you that option. -

    -

    The cutoff/adjust keyword applies only to MSM. If this option is -turned on, the Coulombic cutoff will be automatically adjusted at the -beginning of the run to give the desired estimated error. Other -cutoffs such as LJ will not be affected. If the grid is not set using -the mesh command, this command will also attempt to use the optimal -grid that minimizes cost using an estimate given by -(Hardy). Note that this cost estimate is not exact, somewhat -experimental, and still may not yield the optimal parameters. -

    -

    The pressure/scalar keyword applies only to MSM. If this option is -turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will -be computed, which can be used, for example, to run an isotropic barostat. -Computing the full pressure tensor with MSM is expensive, and this option -provides a faster alternative. The scalar pressure is computed using a -relationship between the Coulombic energy and pressure (Hummer) -instead of using the virial equation. This option cannot be used to access -individual components of the pressure tensor, to compute per-atom virial, -or with suffix kspace/pair styles of MSM, like OMP or GPU. -

    -

    The fftbench keyword applies only to PPPM. It is on by default. If -this option is turned off, LAMMPS will not take the time at the end -of a run to give FFT benchmark timings, and will finish a few seconds -faster than it would if this option were on. -

    -

    The collective keyword applies only to PPPM. It is set to no by -default, except on IBM BlueGene machines. If this option is set to -yes, LAMMPS will use MPI collective operations to remap data for -3d-FFT operations instead of the default point-to-point communication. -This is faster on IBM BlueGene machines, and may also be faster on -other machines if they have an efficient implementation of MPI -collective operations and adequate hardware. -

    -

    The diff keyword specifies the differentiation scheme used by the -PPPM method to compute forces on particles given electrostatic -potentials on the PPPM mesh. The ik approach is the default for -PPPM and is the original formulation used in (Hockney). It -performs differentiation in Kspace, and uses 3 FFTs to transfer each -component of the computed fields back to real space for total of 4 -FFTs per timestep. -

    -

    The analytic differentiation ad approach uses only 1 FFT to transfer -information back to real space for a total of 2 FFTs per timestep. It -then performs analytic differentiation on the single quantity to -generate the 3 components of the electric field at each grid point. -This is sometimes referred to as "smoothed" PPPM. This approach -requires a somewhat larger PPPM mesh to achieve the same accuracy as -the ik method. Currently, only the ik method (default) can be -used for a triclinic simulation cell with PPPM. The ad method is -always used for MSM. -

    -

    IMPORTANT NOTE: Currently, not all PPPM styles support the ad -option. Support for those PPPM variants will be added later. -

    -

    The kmax/ewald keyword sets the number of kspace vectors in each -dimension for kspace style ewald. The three values must be positive -integers, or else (0,0,0), which unsets the option. When this option -is not set, the Ewald sum scheme chooses its own kspace vectors, -consistent with the user-specified accuracy and pairwise cutoff. In -any case, if kspace style ewald is invoked, the values used are -printed to the screen and the log file at the start of the run. -

    -

    With the mix/disp keyword one can select the mixing rule for the -dispersion coefficients. With pair, the dispersion coefficients of -unlike types are computed as indicated with -pair_modify. With geom, geometric mixing is -enforced on the dispersion coefficients in the kspace -coefficients. When using the arithmetic mixing rule, this will -speed-up the simulations but introduces some error in the force -computations, as shown in (Wennberg). With none, it is -assumed that no mixing rule is applicable. Splitting of the dispersion -coefficients will be performed as described in -(Isele-Holder). This splitting can be influenced with -the splittol keywords. Only the eigenvalues that are larger than tol -compared to the largest eigenvalues are included. Using this keywords -the original matrix of dispersion coefficients is approximated. This -leads to faster computations, but the accuracy in the reciprocal space -computations of the dispersion part is decreased. -

    -

    The force/disp/real and force/disp/kspace keywords set the force -accuracy for the real and space computations for the dispersion part -of pppm/disp. As shown in (Isele-Holder), optimal -performance and accuracy in the results is obtained when these values -are different. -

    -

    The disp/auto option controlls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to no, parameters have -to be specified using the gewald/disp, mesh/disp, -force/disp/real or force/disp/kspace keywords, or -the code will stop with an error message. When this option is set to -yes, the error message will not appear and the simulation will start. -For a typical application, using the automatic parameter generation will provide -simulations that are either inaccurate or slow. Using this option is thus not -recommended. For guidelines on how to obtain good parameters, see the How-To discussion. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    kspace_style, boundary -

    -

    Default: -

    -

    The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = -5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0, -gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik -(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0, -split = 0, tol = 1.0e-6, and disp/auto = no. -

    -
    - - - -

    (Hockney) Hockney and Eastwood, Computer Simulation Using Particles, -Adam Hilger, NY (1989). -

    - - -

    (Yeh) Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999). -

    - - -

    (Ballenegger) Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 -(2009). -

    - - -

    (Klapp) Klapp, Schoen, J Chem Phys, 117, 8050 (2002). -

    - - -

    (Hardy) David Hardy thesis: Multilevel Summation for the Fast -Evaluation of Forces for the Simulation of Biomolecules, University of -Illinois at Urbana-Champaign, (2006). -

    - - -

    (Hummer) Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998) -

    - - -

    (Isele-Holder) Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J -Chem Theory Comput, 9, 5412 (2013). -

    - - -

    (Wennberg) Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, -9, 3527 (2013). -

    - diff --git a/doc/doc2/kspace_style.html b/doc/doc2/kspace_style.html deleted file mode 100644 index 36b55dc1da..0000000000 --- a/doc/doc2/kspace_style.html +++ /dev/null @@ -1,394 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    kspace_style command -

    -

    Syntax: -

    -
    kspace_style style value 
-
    -
    • style = none or ewald or ewald/disp or ewald/omp or pppm or pppm/cg or pppm/disp or pppm/tip4p or pppm/stagger or pppm/disp/tip4p or pppm/gpu or pppm/omp or pppm/cg/omp or pppm/tip4p/omp or msm or msm/cg or msm/omp or msm/cg/omp - -
        none value = none
-  ewald value = accuracy
-    accuracy = desired relative error in forces
-  ewald/disp value = accuracy
-    accuracy = desired relative error in forces
-  ewald/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm value = accuracy
-    accuracy = desired relative error in forces
-  pppm/cg value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  pppm/disp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/tip4p value = accuracy
-    accuracy = desired relative error in forces
-  pppm/disp/tip4p value = accuracy
-    accuracy = desired relative error in forces
-  pppm/gpu value = accuracy
-    accuracy = desired relative error in forces
-  pppm/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/cg/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/tip4p/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/stagger value = accuracy
-    accuracy = desired relative error in forces
-  msm value = accuracy
-    accuracy = desired relative error in forces
-  msm/cg value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  msm/omp value = accuracy
-    accuracy = desired relative error in forces
-  msm/cg/omp value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units) 
-
      - -
    -

    Examples: -

    -
    kspace_style pppm 1.0e-4
-kspace_style pppm/cg 1.0e-5 1.0e-6
-kspace style msm 1.0e-4
-kspace_style none 
-
    -

    Description: -

    -

    Define a long-range solver for LAMMPS to use each timestep to compute -long-range Coulombic interactions or long-range 1/r^6 interactions. -Most of the long-range solvers perform their computation in K-space, -hence the name of this command. -

    -

    When such a solver is used in conjunction with an appropriate pair -style, the cutoff for Coulombic or 1/r^N interactions is effectively -infinite. If the Coulombic case, this means each charge in the system -interacts with charges in an infinite array of periodic images of the -simulation domain. -

    -

    Note that using a long-range solver requires use of a matching pair -style to perform consistent short-range pairwise -calculations. This means that the name of the pair style contains a -matching keyword to the name of the KSpace style, as in this table: -

    -
    - - - - -
    Pair style KSpace style
    coul/long ewald or pppm
    coul/msm msm
    lj/long or buck/long disp (for dispersion)
    tip4p/long tip4p -
    - -
    - -

    The ewald style performs a standard Ewald summation as described in -any solid-state physics text. -

    -

    The ewald/disp style adds a long-range dispersion sum option for -1/r^6 potentials and is useful for simulation of interfaces -(Veld). It also performs standard Coulombic Ewald summations, -but in a more efficient manner than the ewald style. The 1/r^6 -capability means that Lennard-Jones or Buckingham potentials can be -used without a cutoff, i.e. they become full long-range potentials. -The ewald/disp style can also be used with point-dipoles -(Toukmaji) and is currently the only kspace solver in -LAMMPS with this capability. -

    -
    - -

    The pppm style invokes a particle-particle particle-mesh solver -(Hockney) which maps atom charge to a 3d mesh, uses 3d FFTs -to solve Poisson's equation on the mesh, then interpolates electric -fields on the mesh points back to the atoms. It is closely related to -the particle-mesh Ewald technique (PME) (Darden) used in -AMBER and CHARMM. The cost of traditional Ewald summation scales as -N^(3/2) where N is the number of atoms in the system. The PPPM solver -scales as Nlog(N) due to the FFTs, so it is almost always a faster -choice (Pollock). -

    -

    The pppm/cg style is identical to the pppm style except that it -has an optimization for systems where most particles are uncharged. -Similarly the msm/cg style implements the same optimization for msm. -The optional smallq argument defines the cutoff for the absolute -charge value which determines whether a particle is considered charged -or not. Its default value is 1.0e-5. -

    -

    The pppm/tip4p style is identical to the pppm style except that it -adds a charge at the massless 4th site in each TIP4P water molecule. -It should be used with pair styles with a -tip4p/long in their style name. -

    -

    The pppm/stagger style performs calculations using two different -meshes, one shifted slightly with respect to the other. This can -reduce force aliasing errors and increase the accuracy of the method -for a given mesh size. Or a coarser mesh can be used for the same -target accuracy, which saves CPU time. However, there is a trade-off -since FFTs on two meshes are now performed which increases the -compuation required. See (Cerutti), (Neelov), -and (Hockney) for details of the method. -

    -

    For high relative accuracy, using staggered PPPM allows the mesh size -to be reduced by a factor of 2 in each dimension as compared to -regular PPPM (for the same target accuracy). This can give up to a 4x -speedup in the KSpace time (8x less mesh points, 2x more expensive). -However, for low relative accuracy, the staggered PPPM mesh size may -be essentially the same as for regular PPPM, which means the method -will be up to 2x slower in the KSpace time (simply 2x more expensive). -For more details and timings, see -Section_accelerate. -

    -

    IMPORTANT NOTE: Using pppm/stagger may not give the same increase in -the accuracy of energy and pressure as it does in forces, so some -caution must be used if energy and/or pressure are quantities of -interest, such as when using a barostat. -

    -
    - -

    The pppm/disp and pppm/disp/tip4p styles add a mesh-based long-range -dispersion sum option for 1/r^6 potentials (Isele-Holder), -similar to the ewald/disp style. The 1/r^6 capability means -that Lennard-Jones or Buckingham potentials can be used without a cutoff, -i.e. they become full long-range potentials. -

    -

    For these styles, you will possibly want to adjust the default choice of -parameters by using the kspace_modify command. -This can be done by either choosing the Ewald and grid parameters, or -by specifying separate accuracies for the real and kspace -calculations. When not making any settings, the simulation will stop with -an error message. Further information on the influence of the parameters -and how to choose them is described in (Isele-Holder), -(Isele-Holder2) and the -How-To discussion. -

    -
    - -

    IMPORTANT NOTE: All of the PPPM styles can be used with -single-precision FFTs by using the compiler switch -DFFT_SINGLE for -the FFT_INC setting in your lo-level Makefile. This setting also -changes some of the PPPM operations (e.g. mapping charge to mesh and -interpolating electric fields to particles) to be performed in single -precision. This option can speed-up long-range calulations, -particularly in parallel or on GPUs. The use of the -DFFT_SINGLE flag -is discussed in this section of the -manual. MSM does not currently support the -DFFT_SINGLE compiler switch. -

    -
    - -

    The msm style invokes a multi-level summation method MSM solver, -(Hardy) or (Hardy2), which maps atom charge to a 3d -mesh, and uses a multi-level hierarchy of coarser and coarser meshes -on which direct coulomb solves are done. This method does not use -FFTs and scales as N. It may therefore be faster than the other -K-space solvers for relatively large problems when running on large -core counts. MSM can also be used for non-periodic boundary conditions and -for mixed periodic and non-periodic boundaries. -

    -

    MSM is most competitive versus Ewald and PPPM when only relatively -low accuracy forces, about 1e-4 relative error or less accurate, -are needed. Note that use of a larger coulomb cutoff (i.e. 15 -angstroms instead of 10 angstroms) provides better MSM accuracy for -both the real space and grid computed forces. -

    -

    Currently calculation of the full pressure tensor in MSM is expensive. -Using the kspace_modify pressure/scalar yes -command provides a less expensive way to compute the scalar pressure -(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example, -to run an isotropic barostat. If the full pressure tensor is needed, -then calculating the pressure at every timestep or using a fixed -pressure simulation with MSM will cause the code to run slower. -

    -
    - -

    The specified accuracy determines the relative RMS error in per-atom -forces calculated by the long-range solver. It is set as a -dimensionless number, relative to the force that two unit point -charges (e.g. 2 monovalent ions) exert on each other at a distance of -1 Angstrom. This reference value was chosen as representative of the -magnitude of electrostatic forces in atomic systems. Thus an accuracy -value of 1.0e-4 means that the RMS error will be a factor of 10000 -smaller than the reference force. -

    -

    The accuracy setting is used in conjunction with the pairwise cutoff -to determine the number of K-space vectors for style ewald or the -grid size for style pppm or msm. -

    -

    Note that style pppm only computes the grid size at the beginning of -a simulation, so if the length or triclinic tilt of the simulation -cell increases dramatically during the course of the simulation, the -accuracy of the simulation may degrade. Likewise, if the -kspace_modify slab option is used with -shrink-wrap boundaries in the z-dimension, and the box size changes -dramatically in z. For example, for a triclinic system with all three -tilt factors set to the maximum limit, the PPPM grid should be -increased roughly by a factor of 1.5 in the y direction and 2.0 in the -z direction as compared to the same system using a cubic orthogonal -simulation cell. One way to ensure the accuracy requirement is being -met is to run a short simulation at the maximum expected tilt or -length, note the required grid size, and then use the -kspace_modify mesh command to manually set the -PPPM grid size to this value. -

    -

    RMS force errors in real space for ewald and pppm are estimated -using equation 18 of (Kolafa), which is also referenced as -equation 9 of (Petersen). RMS force errors in K-space for -ewald are estimated using equation 11 of (Petersen), -which is similar to equation 32 of (Kolafa). RMS force -errors in K-space for pppm are estimated using equation 38 of -(Deserno). RMS force errors for msm are estimated -using ideas from chapter 3 of (Hardy), with equation 3.197 -of particular note. When using msm with non-periodic boundary -conditions, it is expected that the error estimation will be too -pessimistic. RMS force errors for dipoles when using ewald/disp -are estimated using equations 33 and 46 of (Wang). -

    -

    See the kspace_modify command for additional -options of the K-space solvers that can be set, including a force -option for setting an absoulte RMS error in forces, as opposed to a -relative RMS error. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    More specifically, the pppm/gpu style performs charge assignment and -force interpolation calculations on the GPU. These processes are -performed either in single or double precision, depending on whether -the -DFFT_SINGLE setting was specified in your lo-level Makefile, as -discussed above. The FFTs themselves are still calculated on the CPU. -If pppm/gpu is used with a GPU-enabled pair style, part of the PPPM -calculation can be performed concurrently on the GPU while other -calculations for non-bonded and bonded force calculation are performed -on the CPU. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP, and OPT packages respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restrictions: -

    -

    Note that the long-range electrostatic solvers in LAMMPS assume conducting -metal (tinfoil) boundary conditions for both charge and dipole -interactions. Vacuum boundary conditions are not currently supported. -

    -

    The ewald/disp, ewald, pppm, and msm styles support -non-orthogonal (triclinic symmetry) simulation boxes. However, triclinic -simulation cells may not yet be supported by suffix versions of these -styles (such as pppm/cuda). -

    -

    All of the kspace styles are part of the KSPACE package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. Note that -the KSPACE package is installed by default. -

    -

    For MSM, a simulation must be 3d and one can use any combination of -periodic, non-periodic, or shrink-wrapped boundaries (specified using -the boundary command). -

    -

    For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions. -The only exception is if the slab option is set with kspace_modify, -in which case the xy dimensions must be periodic and the z dimension must be -non-periodic. -

    -

    Related commands: -

    -

    kspace_modify, pair_style -lj/cut/coul/long, pair_style -lj/charmm/coul/long, pair_style -lj/long/coul/long, pair_style buck/coul/long -

    -

    Default: -

    -
    kspace_style none 
-
    -
    - - - -

    (Darden) Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993). -

    - - -

    (Deserno) Deserno and Holm, J Chem Phys, 109, 7694 (1998). -

    - - -

    (Hockney) Hockney and Eastwood, Computer Simulation Using Particles, -Adam Hilger, NY (1989). -

    - - -

    (Kolafa) Kolafa and Perram, Molecular Simualtion, 9, 351 (1992). -

    - - -

    (Petersen) Petersen, J Chem Phys, 103, 3668 (1995). -

    - - -

    (Wang) Wang and Holm, J Chem Phys, 115, 6277 (2001). -

    - - -

    (Pollock) Pollock and Glosli, Comp Phys Comm, 95, 93 (1996). -

    - - -

    (Cerutti) Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory -and Computation 5, 2322 (2009) -

    - - -

    (Neelov) Neelov, Holm, J Chem Phys 132, 234103 (2010) -

    - - -

    (Veld) In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007). -

    - - -

    (Toukmaji) Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, -10913 (2000). -

    - - -

    (Isele-Holder) Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012). -

    - - -

    (Isele-Holder2) Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory -Comput 9, 5412 (2013). -

    - - -

    (Hardy) David Hardy thesis: Multilevel Summation for the Fast -Evaluation of Forces for the Simulation of Biomolecules, University of -Illinois at Urbana-Champaign, (2006). -

    - - -

    (Hardy) Hardy, Stone, Schulten, Parallel Computing 35 (2009) -164-177. -

    - diff --git a/doc/doc2/label.html b/doc/doc2/label.html deleted file mode 100644 index 70030e6d3c..0000000000 --- a/doc/doc2/label.html +++ /dev/null @@ -1,41 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    label command -

    -

    Syntax: -

    -
    label ID 
-
    -
    • ID = string used as label name -
    -

    Examples: -

    -
    label xyz
-label loop 
-
    -

    Description: -

    -

    Label this line of the input script with the chosen ID. Unless a jump -command was used previously, this does nothing. But if a -jump command was used with a label argument to begin -invoking this script file, then all command lines in the script prior -to this line will be ignored. I.e. execution of the script will begin -at this line. This is useful for looping over a section of the input -script as discussed in the jump command. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/lattice.html b/doc/doc2/lattice.html deleted file mode 100644 index c876428439..0000000000 --- a/doc/doc2/lattice.html +++ /dev/null @@ -1,300 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    lattice command -

    -

    Syntax: -

    -
    lattice style scale keyword values ... 
-
    -
    • style = none or sc or bcc or fcc or hcp or diamond or sq or sq2 or hex or custom - -
    • scale = scale factor between lattice and simulation box - -
        scale = reduced density rho* (for LJ units)
-  scale = lattice constant in distance units (for all other units) 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = origin or orient or spacing or a1 or a2 or a3 or basis - -
        origin values = x y z
-    x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
-  orient values = dim i j k
-    dim = x or y or z
-    i,j,k = integer lattice directions
-  spacing values = dx dy dz
-    dx,dy,dz = lattice spacings in the x,y,z box directions
-  a1,a2,a3 values = x y z
-    x,y,z = primitive vector components that define unit cell
-  basis values = x y z
-    x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) 
-
      - -
    -

    Examples: -

    -
    lattice fcc 3.52
-lattice hex 0.85
-lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
-lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
-                    basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
-lattice none 2.0 
-
    -

    Description: -

    -

    Define a lattice for use by other commands. In LAMMPS, a lattice is -simply a set of points in space, determined by a unit cell with basis -atoms, that is replicated infinitely in all dimensions. The arguments -of the lattice command can be used to define a wide variety of -crystallographic lattices. -

    -

    A lattice is used by LAMMPS in two ways. First, the -create_atoms command creates atoms on the lattice -points inside the simulation box. Note that the -create_atoms command allows different atom types -to be assigned to different basis atoms of the lattice. Second, the -lattice spacing in the x,y,z dimensions implied by the lattice, can be -used by other commands as distance units -(e.g. create_box, region and -velocity), which are often convenient to use when the -underlying problem geometry is atoms on a lattice. -

    -

    The lattice style must be consistent with the dimension of the -simulation - see the dimension command. Styles sc -or bcc or fcc or hcp or diamond are for 3d problems. Styles -sq or sq2 or hex are for 2d problems. Style custom can be -used for either 2d or 3d problems. -

    -

    A lattice consists of a unit cell, a set of basis atoms within that -cell, and a set of transformation parameters (scale, origin, orient) -that map the unit cell into the simulation box. The vectors a1,a2,a3 -are the edge vectors of the unit cell. This is the nomenclature for -"primitive" vectors in solid-state crystallography, but in LAMMPS the -unit cell they determine does not have to be a "primitive cell" of -minimum volume. -

    -

    Note that the lattice command can be used multiple times in an input -script. Each time it is invoked, the lattice attributes are -re-defined and are used for all subsequent commands (that use lattice -attributes). For example, a sequence of lattice, -region, and create_atoms commands -can be repeated multiple times to build a poly-crystalline model with -different geometric regions populated with atoms in different lattice -orientations. -

    -
    - -

    A lattice of style none does not define a unit cell and basis set, -so it cannot be used with the create_atoms -command. However it does define a lattice spacing via the specified -scale parameter. As explained above the lattice spacings in x,y,z can -be used by other commands as distance units. No additional -keyword/value pairs can be specified for the none style. By -default, a "lattice none 1.0" is defined, which means the lattice -spacing is the same as one distance unit, as defined by the -units command. -

    -

    Lattices of style sc, fcc, bcc, and diamond are 3d lattices -that define a cubic unit cell with edge length = 1.0. This means a1 = -1 0 0, a2 = 0 1 0, and a3 = 0 0 1. Style hcp has a1 = 1 0 0, a2 = 0 -sqrt(3) 0, and a3 = 0 0 sqrt(8/3). The placement of the basis atoms -within the unit cell are described in any solid-state physics text. A -sc lattice has 1 basis atom at the lower-left-bottom corner of the -cube. A bcc lattice has 2 basis atoms, one at the corner and one at -the center of the cube. A fcc lattice has 4 basis atoms, one at the -corner and 3 at the cube face centers. A hcp lattice has 4 basis -atoms, two in the z = 0 plane and 2 in the z = 0.5 plane. A diamond -lattice has 8 basis atoms. -

    -

    Lattices of style sq and sq2 are 2d lattices that define a square -unit cell with edge length = 1.0. This means a1 = 1 0 0 and a2 = 0 1 -0. A sq lattice has 1 basis atom at the lower-left corner of the -square. A sq2 lattice has 2 basis atoms, one at the corner and one -at the center of the square. A hex style is also a 2d lattice, but -the unit cell is rectangular, with a1 = 1 0 0 and a2 = 0 sqrt(3) 0. -It has 2 basis atoms, one at the corner and one at the center of the -rectangle. -

    -

    A lattice of style custom allows you to specify a1, a2, a3, and a -list of basis atoms to put in the unit cell. By default, a1 and a2 -and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you -can specify them to be of any length and non-orthogonal to each other, -so that they describe a tilted parallelepiped. Via the basis -keyword you add atoms, one at a time, to the unit cell. Its arguments -are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector -x of a basis atom within the unit cell is thus a linear combination of -the the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, -where bx,by,bz are the 3 values specified for the basis keyword. -

    -
    - -

    This sub-section discusses the arguments that determine how the -idealized unit cell is transformed into a lattice of points within the -simulation box. -

    -

    The scale argument determines how the size of the unit cell will be -scaled when mapping it into the simulation box. I.e. it determines a -multiplicative factor to apply to the unit cell, to convert it to a -lattice of the desired size and distance units in the simulation box. -The meaning of the scale argument depends on the units -being used in your simulation. -

    -

    For all unit styles except lj, the scale argument is specified in -the distance units defined by the unit style. For example, in real -or metal units, if the unit cell is a unit cube with edge length -1.0, specifying scale = 3.52 would create a cubic lattice with a -spacing of 3.52 Angstroms. In cgs units, the spacing would be 3.52 -cm. -

    -

    For unit style lj, the scale argument is the Lennard-Jones reduced -density, typically written as rho*. LAMMPS converts this value into -the multiplicative factor via the formula "factor^dim = rho/rho*", -where rho = N/V with V = the volume of the lattice unit cell and N = -the number of basis atoms in the unit cell (described below), and dim -= 2 or 3 for the dimensionality of the simulation. Effectively, this -means that if LJ particles of size sigma = 1.0 are used in the -simulation, the lattice of particles will be at the desired reduced -density. -

    -

    The origin option specifies how the unit cell will be shifted or -translated when mapping it into the simulation box. The x,y,z values -are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice -by a fraction of the lattice spacing in each dimension. The meaning -of "lattice spacing" is discussed below. -

    -

    The orient option specifies how the unit cell will be rotated when -mapping it into the simulation box. The dim argument is one of the -3 coordinate axes in the simulation box. The other 3 arguments are -the crystallographic direction in the lattice that you want to orient -along that axis, specified as integers. E.g. "orient x 2 1 0" means -the x-axis in the simulation box will be the [210] lattice -direction, and similarly for y and z. The 3 lattice directions you -specify do not have to be unit vectors, but they must be mutually -orthogonal and obey the right-hand rule, i.e. (X cross Y) points in -the Z direction. -

    -

    IMPORTANT NOTE: The preceding paragraph describing lattice directions -is only valid for orthogonal cubic unit cells (or square in 2d). If -you are using a hcp or hex lattice or the more general lattice -style custom with non-orthogonal a1,a2,a3 vectors, then you should -think of the 3 orient vectors as creating a 3x3 rotation matrix -which is applied to a1,a2,a3 to rotate the original unit cell to a new -orientation in the simulation box. -

    -
    - -

    Several LAMMPS commands have the option to use distance units that are -inferred from "lattice spacings" in the x,y,z box directions. -E.g. the region command can create a block of size -10x20x20, where 10 means 10 lattice spacings in the x direction. -

    -

    IMPORTANT NOTE: Though they are called lattice spacings, all the -commands that have a "units lattice" option, simply use the 3 values -as scale factors on the distance units defined by the -units command. Thus if you do not like the lattice -spacings computed by LAMMPS (e.g. for a non-orthogonal or rotated unit -cell), you can define the 3 values to be whatever you wish, via the -spacing option. -

    -

    If the spacing option is not specified, the lattice spacings are -computed by LAMMPS in the following way. A unit cell of the lattice -is mapped into the simulation box (scaled and rotated), so that it now -has (perhaps) a modified size and orientation. The lattice spacing in -X is defined as the difference between the min/max extent of the x -coordinates of the 8 corner points of the modified unit cell (4 in -2d). Similarly, the Y and Z lattice spacings are defined as the -difference in the min/max of the y and z coordinates. -

    -

    Note that if the unit cell is orthogonal with axis-aligned edges (no -rotation via the orient keyword), then the lattice spacings in each -dimension are simply the scale factor (described above) multiplied by -the length of a1,a2,a3. Thus a hex style lattice with a scale -factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and -3*sqrt(3.0) in y. -

    -

    IMPORTANT NOTE: For non-orthogonal unit cells and/or when a rotation -is applied via the orient keyword, then the lattice spacings -computed by LAMMPS are typically less intuitive. In particular, in -these cases, there is no guarantee that a particular lattice spacing -is an integer multiple of the periodicity of the lattice in that -direction. Thus, if you create an orthogonal periodic simulation box -whose size in a dimension is a multiple of the lattice spacing, and -then fill it with atoms via the create_atoms -command, you will NOT necessarily create a periodic system. -I.e. atoms may overlap incorrectly at the faces of the simulation box. -

    -

    The spacing option sets the 3 lattice spacings directly. All must -be non-zero (use 1.0 for dz in a 2d simulation). The specified values -are multiplied by the multiplicative factor described above that is -associated with the scale factor. Thus a spacing of 1.0 means one -unit cell edge length independent of the scale factor. As mentioned -above, this option can be useful if the spacings LAMMPS computes are -inconvenient to use in subsequent commands, which can be the case for -non-orthogonal or rotated lattices. -

    -

    Note that whenever the lattice command is used, the values of the -lattice spacings LAMMPS calculates are printed out. Thus their effect -in commands that use the spacings should be decipherable. -

    -
    - -

    Example commands for generating a Wurtzite crystal (courtesy -of Aidan Thompson), with its 8 atom unit cell. -

    -
    variable a equal  4.340330
-variable b equal  $a*sqrt(3.0)
-variable c equal  $a*sqrt(8.0/3.0) 
-
    -
    variable 1_3 equal 1.0/3.0
-variable 2_3 equal 2.0/3.0
-variable 1_6 equal 1.0/6.0
-variable 5_6 equal 5.0/6.0
-variable 1_12 equal 1.0/12.0
-variable 5_12 equal 5.0/12/0 
-
    -
    lattice custom    1.0     &
-        a1      $a      0.0     0.0     &
-        a2      0.0     $b      0.0     &
-        a3      0.0     0.0     $c      &
-        basis   0.0     0.0     0.0     &
-        basis   0.5     0.5     0.0     &
-        basis   ${1_3}  0.0     0.5     &
-        basis   ${5_6}  0.5     0.5     &
-        basis   0.0     0.0     0.625   &
-        basis   0.5     0.5     0.625   &
-        basis   ${1_3}  0.0     0.125   &
-        basis   ${5_6}  0.5     0.125 
-
    -
    region myreg block 0 1 0 1 0 1
-create_box      2 myreg
-create_atoms    1 box 
-
    -
    - -

    Restrictions: -

    -

    The a1,a2,a3,basis keywords can only be used with style custom. -

    -

    Related commands: -

    -

    dimension, create_atoms, -region -

    -

    Default: -

    -
    lattice none 1.0 
-
    -

    For other lattice styles, the option defaults are origin = 0.0 0.0 -0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1 0 0, -a2 = 0 1 0, and a3 = 0 0 1. -

    - diff --git a/doc/doc2/log.html b/doc/doc2/log.html deleted file mode 100644 index e583a10ea3..0000000000 --- a/doc/doc2/log.html +++ /dev/null @@ -1,51 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    log command -

    -

    Syntax: -

    -
    log file keyword 
-
    -
    • file = name of new logfile -
    • keyword = append if output should be appended to logfile (optional) -
    -

    Examples: -

    -
    log log.equil
-log log.equil append 
-
    -

    Description: -

    -

    This command closes the current LAMMPS log file, opens a new file with -the specified name, and begins logging information to it. If the -specified file name is none, then no new log file is opened. If the -optional keyword append is specified, then output will be appended -to an existing log file, instead of overwriting it. -

    -

    If multiple processor partitions are being used, the file name should -be a variable, so that different processors do not attempt to write to -the same log file. -

    -

    The file "log.lammps" is the default log file for a LAMMPS run. The -name of the initial log file can also be set by the command-line -switch -log. See Section_start 6 for -details. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: -

    -

    The default LAMMPS log file is named log.lammps -

    - diff --git a/doc/doc2/mass.html b/doc/doc2/mass.html deleted file mode 100644 index 1fa0e43775..0000000000 --- a/doc/doc2/mass.html +++ /dev/null @@ -1,89 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    mass command -

    -

    Syntax: -

    -
    mass I value 
-
    -
    • I = atom type (see asterisk form below) -
    • value = mass -
    -

    Examples: -

    -
    mass 1 1.0
-mass * 62.5
-mass 2* 62.5 
-
    -

    Description: -

    -

    Set the mass for all atoms of one or more atom types. Per-type mass -values can also be set in the read_data data file -using the "Masses" keyword. See the units command for -what mass units to use. -

    -

    The I index can be specified in one of two ways. An explicit numeric -value can be used, as in the 1st example above. Or a wild-card -asterisk can be used to set the mass for multiple atom types. This -takes the form "*" or "*n" or "n*" or "m*n". If N = the number of -atom types, then an asterisk with no numeric values means all types -from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). -

    -

    A line in a data file that follows the "Masses" -keyword specifies mass using the same format as the arguments of the -mass command in an input script, except that no wild-card asterisk can -be used. For example, under the "Masses" section of a data file, the -line that corresponds to the 1st example above would be listed as -

    -
    1 1.0 
-
    -

    Note that the mass command can only be used if the atom -style requires per-type atom mass to be set. -Currently, all but the sphere and ellipsoid and peri styles do. -They require mass to be set for individual particles, not types. -Per-atom masses are defined in the data file read by the -read_data command, or set to default values by the -create_atoms command. Per-atom masses can also be -set to new values by the set mass or set density -commands. -

    -

    Also note that pair_style eam and pair_style -bop commands define the masses of atom types in their -respective potential files, in which case the mass command is normally -not used. -

    -

    If you define a hybrid atom style which includes one -(or more) sub-styles which require per-type mass and one (or more) -sub-styles which require per-atom mass, then you must define both. -However, in this case the per-type mass will be ignored; only the -per-atom mass will be used by LAMMPS. -

    -

    Restrictions: -

    -

    This command must come after the simulation box is defined by a -read_data, read_restart, or -create_box command. -

    -

    All masses must be defined before a simulation is run. They must also -all be defined before a velocity or fix -shake command is used. -

    -

    The mass assigned to any type or atom must be > 0.0. -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/min_modify.html b/doc/doc2/min_modify.html deleted file mode 100644 index d9298f9b69..0000000000 --- a/doc/doc2/min_modify.html +++ /dev/null @@ -1,83 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    min_modify command -

    -

    Syntax: -

    -
    min_modify keyword values ... 
-
    -
    • one or more keyword/value pairs may be listed - -
      keyword = dmax or line
-  dmax value = max
-    max = maximum distance for line search to move (distance units)
-  line value = backtrack or quadratic or forcezero
-    backtrack,quadratic,forcezero = style of linesearch to use 
-
      - -
    -

    Examples: -

    -
    min_modify dmax 0.2 
-
    -

    Description: -

    -

    This command sets parameters that affect the energy minimization -algorithms selected by the min_style command. The -various settings may affect the convergence rate and overall number of -force evaluations required by a minimization, so users can experiment -with these parameters to tune their minimizations. -

    -

    The cg and sd minimization styles have an outer iteration and an -inner iteration which is steps along a one-dimensional line search in -a particular search direction. The dmax parameter is how far any -atom can move in a single line search in any dimension (x, y, or z). -For the quickmin and fire minimization styles, the dmax setting -is how far any atom can move in a single iteration (timestep). Thus a -value of 0.1 in real units means no atom will move -further than 0.1 Angstroms in a single outer iteration. This prevents -highly overlapped atoms from being moved long distances (e.g. through -another atom) due to large forces. -

    -

    The choice of line search algorithm for the cg and sd minimization -styles can be selected via the line keyword. -The default quadratic line search algorithm starts out using -the robust backtracking method described below. However, once -the system gets close to a local -minimum and the linesearch steps get small, so that the energy -is approximately quadratic in the step length, it uses the -estimated location of zero gradient as the linesearch step, -provided the energy change is downhill. -This becomes more efficient than backtracking -for highly-converged relaxations. The forcezero -line search algorithm is similar to quadratic. -It may be more efficient than quadratic on some systems. -

    -

    The backtracking search is robust and should always find a local energy -minimum. However, it will "converge" when it can no longer reduce the -energy of the system. Individual atom forces may still be larger than -desired at this point, because the energy change is measured as the -difference of two large values (energy before and energy after) and -that difference may be smaller than machine epsilon even if atoms -could move in the gradient direction to reduce forces further. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    min_style, minimize -

    -

    Default: -

    -

    The option defaults are dmax = 0.1 and line = quadratic. -

    - diff --git a/doc/doc2/min_style.html b/doc/doc2/min_style.html deleted file mode 100644 index 740ca261e1..0000000000 --- a/doc/doc2/min_style.html +++ /dev/null @@ -1,104 +0,0 @@ - -
    LAMMPS WWW Page - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    min_style command -

    -

    Syntax: -

    -
    min_style style 
-
    -
    • style = cg or hftn or sd or quickmin or fire -
    -

    Examples: -

    -
    min_style cg
-min_style fire 
-
    -

    Description: -

    -

    Choose a minimization algorithm to use when a minimize -command is performed. -

    -

    Style cg is the Polak-Ribiere version of the conjugate gradient (CG) -algorithm. At each iteration the force gradient is combined with the -previous iteration information to compute a new search direction -perpendicular (conjugate) to the previous search direction. The PR -variant affects how the direction is chosen and how the CG method is -restarted when it ceases to make progress. The PR variant is thought -to be the most effective CG choice for most problems. -

    -

    Style hftn is a Hessian-free truncated Newton algorithm. At each -iteration a quadratic model of the energy potential is solved by a -conjugate gradient inner iteration. The Hessian (second derivatives) -of the energy is not formed directly, but approximated in each -conjugate search direction by a finite difference directional -derivative. When close to an energy minimum, the algorithm behaves -like a Newton method and exhibits a quadratic convergence rate to high -accuracy. In most cases the behavior of hftn is similar to cg, -but it offers an alternative if cg seems to perform poorly. This -style is not affected by the min_modify command. -

    -

    Style sd is a steepest descent algorithm. At each iteration, the -search direction is set to the downhill direction corresponding to the -force vector (negative gradient of energy). Typically, steepest -descent will not converge as quickly as CG, but may be more robust in -some situations. -

    -

    Style quickmin is a damped dynamics method described in -(Sheppard), where the damping parameter is related to the -projection of the velocity vector along the current force vector for -each atom. The velocity of each atom is initialized to 0.0 by this -style, at the beginning of a minimization. -

    -

    Style fire is a damped dynamics method described in -(Bitzek), which is similar to quickmin but adds a variable -timestep and alters the projection operation to maintain components of -the velocity non-parallel to the current force vector. The velocity -of each atom is initialized to 0.0 by this style, at the beginning of -a minimization. -

    -

    Either the quickmin and fire styles are useful in the context of -nudged elastic band (NEB) calculations via the neb command. -

    -

    IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep -you have defined via the timestep command. Often they -will converge more quickly if you use a timestep about 10x larger than -you would normally use for dynamics simulations. -

    -

    IMPORTANT NOTE: The quickmin and fire styles do not yet support -the use of the fix box/relax command or -minimizations involving the electron radius in eFF -models. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    min_modify, minimize, neb -

    -

    Default: -

    -
    min_style cg 
-
    -
    - - - -

    (Sheppard) Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 -(2008). See ref 1 in this paper for original reference to Qmin in -Jonsson, Mills, Jacobsen. -

    - - -

    (Bitzek) Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, -97, 170201 (2006). -

    - diff --git a/doc/doc2/minimize.html b/doc/doc2/minimize.html deleted file mode 100644 index 16f8be7b46..0000000000 --- a/doc/doc2/minimize.html +++ /dev/null @@ -1,279 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    minimize command -

    -

    Syntax: -

    -
    minimize etol ftol maxiter maxeval 
-
    -
    • etol = stopping tolerance for energy (unitless) -
    • ftol = stopping tolerance for force (force units) -
    • maxiter = max iterations of minimizer -
    • maxeval = max number of force/energy evaluations -
    -

    Examples: -

    -
    minimize 1.0e-4 1.0e-6 100 1000
-minimize 0.0 1.0e-8 1000 100000 
-
    -

    Description: -

    -

    Perform an energy minimization of the system, by iteratively adjusting -atom coordinates. Iterations are terminated when one of the stopping -criteria is satisfied. At that point the configuration will hopefully -be in local potential energy minimum. More precisely, the -configuration should approximate a critical point for the objective -function (see below), which may or may not be a local minimum. -

    -

    The minimization algorithm used is set by the -min_style command. Other options are set by the -min_modify command. Minimize commands can be -interspersed with run commands to alternate between -relaxation and dynamics. The minimizers bound the distance atoms move -in one iteration, so that you can relax systems with highly overlapped -atoms (large energies and forces) by pushing the atoms off of each -other. -

    -

    Alternate means of relaxing a system are to run dynamics with a small -or limited timestep. Or dynamics can be run -using fix viscous to impose a damping force that -slowly drains all kinetic energy from the system. The pair_style -soft potential can be used to un-overlap atoms while -running dynamics. -

    -

    Note that you can minimize some atoms in the system while holding the -coordiates of other atoms fixed by applying fix -setforce to the other atoms. See a fuller -discussion of using fixes while minimizing below. -

    -

    The minimization styles cg, sd, and hftn -involves an outer iteration loop which sets the search direction along -which atom coordinates are changed. An inner iteration is then -performed using a line search algorithm. The line search typically -evaluates forces and energies several times to set new coordinates. -Currently, a backtracking algorithm is used which may not be optimal -in terms of the number of force evaulations performed, but appears to -be more robust than previous line searches we've tried. The -backtracking method is described in Nocedal and Wright's Numerical -Optimization (Procedure 3.1 on p 41). -

    -

    The minimization styles quickmin and fire perform -damped dynamics using an Euler integration step. Thus they require a -timestep be defined. -

    -

    IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep -you have defined via the timestep command. Often they -will converge more quickly if you use a timestep about 10x larger than -you would normally use for dynamics simulations. -

    -
    - -

    In all cases, the objective function being minimized is the total -potential energy of the system as a function of the N atom -coordinates: -

    -
    -
    -

    where the first term is the sum of all non-bonded pairwise -interactions including long-range Coulombic -interactions, the 2nd thru 5th terms are -bond, angle, -dihedral, and improper -interactions respectively, and the last term is energy due to -fixes which can act as constraints or apply force to atoms, -such as thru interaction with a wall. See the discussion below about -how fix commands affect minimization. -

    -

    The starting point for the minimization is the current configuration -of the atoms. -

    -
    - -

    The minimization procedure stops if any of several criteria are met: -

    -
    • the change in energy between outer iterations is less than etol -
    • the 2-norm (length) of the global force vector is less than the ftol -
    • the line search fails because the step distance backtracks to 0.0 -
    • the number of outer iterations or timesteps exceeds maxiter -
    • the number of total force evaluations exceeds maxeval -
    -

    For the first criterion, the specified energy tolerance etol is -unitless; it is met when the energy change between successive -iterations divided by the energy magnitude is less than or equal to -the tolerance. For example, a setting of 1.0e-4 for etol means an -energy tolerance of one part in 10^4. For the damped dynamics -minimizers this check is not performed for a few steps after -velocities are reset to 0, otherwise the minimizer would prematurely -converge. -

    -

    For the second criterion, the specified force tolerance ftol is in -force units, since it is the length of the global force vector for all -atoms, e.g. a vector of size 3N for N atoms. Since many of the -components will be near zero after minimization, you can think of -ftol as an upper bound on the final force on any component of any -atom. For example, a setting of 1.0e-4 for ftol means no x, y, or z -component of force on any atom will be larger than 1.0e-4 (in force -units) after minimization. -

    -

    Either or both of the etol and ftol values can be set to 0.0, in -which case some other criterion will terminate the minimization. -

    -

    During a minimization, the outer iteration count is treated as a -timestep. Output is triggered by this timestep, e.g. thermodynamic -output or dump and restart files. -

    -

    Using the thermo_style custom command with the -fmax or fnorm keywords can be useful for monitoring the progress -of the minimization. Note that these outputs will be calculated only -from forces on the atoms, and will not include any extra degrees of -freedom, such as from the fix box/relax command. -

    -

    Following minimization, a statistical summary is printed that lists -which convergence criterion caused the minimizer to stop, as well as -information about the energy, force, final line search, and -iteration counts. An example is as follows: -

    -
    Minimization stats:
-  Stopping criterion = max iterations
-  Energy initial, next-to-last, final = 
-       -0.626828169302     -2.82642039062     -2.82643549739
-  Force two-norm initial, final = 2052.1 91.9642
-  Force max component initial, final = 346.048 9.78056
-  Final line search alpha, max atom move = 2.23899e-06 2.18986e-05
-  Iterations, force evaluations = 2000 12724 
-
    -

    The 3 energy values are for before and after the minimization and on -the next-to-last iteration. This is what the etol parameter checks. -

    -

    The two-norm force values are the length of the global force vector -before and after minimization. This is what the ftol parameter -checks. -

    -

    The max-component force values are the absolute value of the largest -component (x,y,z) in the global force vector, i.e. the infinity-norm -of the force vector. -

    -

    The alpha parameter for the line-search, when multiplied by the max -force component (on the last iteration), gives the max distance any -atom moved during the last iteration. Alpha will be 0.0 if the line -search could not reduce the energy. Even if alpha is non-zero, if the -"max atom move" distance is tiny compared to typical atom coordinates, -then it is possible the last iteration effectively caused no atom -movement and thus the evaluated energy did not change and the -minimizer terminated. Said another way, even with non-zero forces, -it's possible the effect of those forces is to move atoms a distance -less than machine precision, so that the energy cannot be further -reduced. -

    -

    The iterations and force evaluation values are what is checked by the -maxiter and maxeval parameters. -

    -
    - -

    IMPORTANT NOTE: There are several force fields in LAMMPS which have -discontinuities or other approximations which may prevent you from -performing an energy minimization to high tolerances. For example, -you should use a pair style that goes to 0.0 at the -cutoff distance when performing minimization (even if you later change -it when running dynamics). If you do not do this, the total energy of -the system will have discontinuities when the relative distance -between any pair of atoms changes from cutoff+epsilon to -cutoff-epsilon and the minimizer may behave poorly. Some of the -manybody potentials use splines and other internal cutoffs that -inherently have this problem. The long-range Coulombic -styles (PPPM, Ewald) are approximate to within the -user-specified tolerance, which means their energy and forces may not -agree to a higher precision than the Kspace-specified tolerance. In -all these cases, the minimizer may give up and stop before finding a -minimum to the specified energy or force tolerance. -

    -

    Note that a cutoff Lennard-Jones potential (and others) can be shifted -so that its energy is 0.0 at the cutoff via the -pair_modify command. See the doc pages for -inidividual pair styles for details. Note that -Coulombic potentials always have a cutoff, unless versions with a -long-range component are used (e.g. pair_style -lj/cut/coul/long). The CHARMM potentials go to 0.0 at -the cutoff (e.g. pair_style lj/charmm/coul/charmm), -as do the GROMACS potentials (e.g. pair_style -lj/gromacs). -

    -

    If a soft potential (pair_style soft) is used the -Astop value is used for the prefactor (no time dependence). -

    -

    The fix box/relax command can be used to apply an -external pressure to the simulation box and allow it to shrink/expand -during the minimization. -

    -

    Only a few other fixes (typically those that apply force constraints) -are invoked during minimization. See the doc pages for individual -fix commands to see which ones are relevant. Current -examples of fixes that can be used include: -

    - -

    IMPORTANT NOTE: Some fixes which are invoked during minimization have -an associated potential energy. For that energy to be included in the -total potential energy of the system (the quantity being minimized), -you MUST enable the fix_modify energy option for -that fix. The doc pages for individual fix commands -specify if this should be done. -

    -
    - -

    Restrictions: -

    -

    Features that are not yet implemented are listed here, in case someone -knows how they could be coded: -

    -

    It is an error to use fix shake with minimization -because it turns off bonds that should be included in the potential -energy of the system. The effect of a fix shake can be approximated -during a minimization by using stiff spring constants for the bonds -and/or angles that would normally be constrained by the SHAKE -algorithm. -

    -

    Fix rigid is also not supported by minimization. It -is not an error to have it defined, but the energy minimization will -not keep the defined body(s) rigid during the minimization. Note that -if bonds, angles, etc internal to a rigid body have been turned off -(e.g. via neigh_modify exclude), they will not -contribute to the potential energy which is probably not what is -desired. -

    -

    Pair potentials that produce torque on a particle (e.g. granular -potentials or the GayBerne -potential for ellipsoidal particles) are not -relaxed by a minimization. More specifically, radial relaxations are -induced, but no rotations are induced by a minimization, so such a -system will not fully relax. -

    -

    Related commands: -

    -

    min_modify, min_style, -run_style -

    -

    Default: none -

    - diff --git a/doc/doc2/molecule.html b/doc/doc2/molecule.html deleted file mode 100644 index 1206839335..0000000000 --- a/doc/doc2/molecule.html +++ /dev/null @@ -1,473 +0,0 @@ - -
    <LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    molecule command -

    -

    Syntax: -

    -
    molecule ID file1 keyword values ... file2 keyword values ... fileN ... 
-
    -
    • ID = user-assigned name for the molecule template - -
    • file1,file2,... = names of files containing molecule descriptions - -
    • zero or more keyword/value pairs may be appended after each file - -
    • keyword = offset or toff or boff or aoff or doff or ioff or scale - -
        offset values = Toff Boff Aoff Doff Ioff
-    Toff = offset to add to atom types
-    Boff = offset to add to bond types
-    Aoff = offset to add to angle types
-    Doff = offset to add to dihedral types
-    Ioff = offset to add to improper types
-  toff value = Toff
-    Toff = offset to add to atom types
-  boff value = Boff
-    Boff = offset to add to bond types
-  aoff value = Aoff
-    Aoff = offset to add to angle types
-  doff value = Doff
-    Doff = offset to add to dihedral types
-  ioff value = Ioff
-    Ioff = offset to add to improper types
-  scale value = sfactor
-    sfactor = scale factor to apply to the size and mass of the molecule 
-
      - -
    -

    Examples: -

    -
    molecule 1 mymol.txt
-molecule 1 co2.txt h2o.txt
-molecule CO2 co2.txt boff 3 aoff 2
-molecule 1 mymol.txt offset 6 9 18 23 14 
-molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3 
-
    -
    -
    -

    Description: -

    -

    Define a molecule template that can be used as part of other LAMMPS -commands, typically to define a collection of particles as a bonded -molecule or a rigid body. Commands that currently use molecule -templates include: -

    - -

    The ID of a molecule template can only contain alphanumeric characters -and underscores. -

    -

    A single template can contain multiple molecules, listed one per file. -Some of the commands listed above currently use only the first -molecule in the template, and will issue a warning if the template -contains multiple molecules. The atom_style -template command allows multiple-molecule templates -to define a system with more than one templated molecule. -

    -

    Each filename can be followed by optional keywords which are applied -only to the molecule in the file as used in this template. This is to -make it easy to use the same molecule file in different molecule -templates or in different simulations. You can specify the same file -multiple times with different optional keywords. -

    -

    The offset, toff, aoff, doff, ioff keywords add the -specified offset values to the atom types, bond types, angle types, -dihedral types, and/or improper types as they are read from the -molecule file. E.g. if toff = 2, and the file uses atom types -1,2,3, then each created molecule will have atom types 3,4,5. For the -offset keyword, all five offset values must be specified, but -individual values will be ignored if the molecule template does not -use that attribute (e.g. no bonds). -

    -

    The scale keyword scales the size of the molecule. This can be -useful for modeling polydisperse granular rigid bodies. The scale -factor is applied to each of these properties in the molecule file, if -they are defined: the individual particle coordinates (Coords -section), the individual mass of each particle (Masses section), the -individual diameters of each particle (Diameters section), the total -mass of the molecule (header keyword = mass), the center-of-mass of -the molecule (header keyword = com), and the moments of inertia of the -molecule (header keyword = inertia). -

    -

    IMPORTANT NOTE: The molecule command can be used to define molecules -with bonds, angles, dihedrals, imporopers, or special bond lists of -neighbors within a molecular topology, so that you can later add the -molecules to your simulation, via one or more of the commands listed -above. If such molecules do not already exist when LAMMPS creates the -simulation box, via the create_box or -read_data command, when you later add them you may -overflow the pre-allocated data structures which store molecular -topology information with each atom, and an error will be generated. -Both the create_box command and the data files read -by the read_data command have "extra" options which -insure space is allocated for storing topology info for molecules that -are added later. -

    -

    The format of an individual molecule file is similar to the data file -read by the read_data commands, and is as follows. -

    -

    A molecule file has a header and a body. The header appears first. -The first line of the header is always skipped; it typically contains -a description of the file. Then lines are read one at a time. Lines -can have a trailing comment starting with '#' that is ignored. If the -line is blank (only whitespace after comment is deleted), it is -skipped. If the line contains a header keyword, the corresponding -value(s) is read from the line. If it doesn't contain a header -keyword, the line begins the body of the file. -

    -

    The body of the file contains zero or more sections. The first line -of a section has only a keyword. The next line is skipped. The -remaining lines of the section contain values. The number of lines -depends on the section keyword as described below. Zero or more blank -lines can be used between sections. Sections can appear in any order, -with a few exceptions as noted below. -

    -

    These are the recognized header keywords. Header lines can come in -any order. The numeric value(s) are read from the beginning of the -line. The keyword should appear at the end of the line. All these -settings have default values, as explained below. A line need only -appear if the value(s) are different than the default. -

    -
    • N atoms = # of atoms N in molecule, default = 0 -
    • Nb bonds = # of bonds Nb in molecule, default = 0 -
    • Na angles = # of angles Na in molecule, default = 0 -
    • Nd dihedrals = # of dihedrals Nd in molecule, default = 0 -
    • Ni impropers = # of impropers Ni in molecule, default = 0 -
    • Mtotal mass = total mass of molecule -
    • Xc Yc Zc com = coordinates of center-of-mass of molecule -
    • Ixx Iyy Izz Ixy Ixz Iyz inertia = 6 components of inertia tensor of molecule -
    -

    For mass, com, and inertia, the default is for LAMMPS to -calculate this quantity itself if needed, assuming the molecules -consists of a set of point particles or finite-size particles (with a -non-zero diameter) that do not overlap. If finite-size particles in -the molecule do overlap, LAMMPS will not account for the overlap -effects when calculating any of these 3 quantities, so you should -pre-compute them yourself and list the values in the file. -

    -

    The mass and center-of-mass coordinates (Xc,Yc,Zc) are -self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) -should be the values consistent with the current orientation of the -rigid body around its center of mass. The values are with respect to -the simulation box XYZ axes, not with respect to the prinicpal axes of -the rigid body itself. LAMMPS performs the latter calculation -internally. -

    -

    These are the allowed section keywords for the body of the file. -

    -
    • Coords, Types, Charges, Diameters, Masses = atom-property sections -
    • Bonds, Angles, Dihedrals, Impropers = molecular topology sections -
    • Special Bond Counts, Special Bonds = special neighbor info -
    • Shake Flags, Shake Atoms, Shake Bond Types = SHAKE info -
    -

    If a Bonds section is specified then the Special Bond Counts and -Special Bonds sections can also be used, if desired, to explicitly -list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see -details below). This is optional since if these sections are not -included, LAMMPS will auto-generate this information. Note that -LAMMPS uses this info to properly exclude or weight bonded pairwise -interactions between bonded atoms. See the -special_bonds command for more details. One -reason to list the special bond info explicitly is for the -thermalized Drude oscillator model which treats -the bonds between nuclear cores and Drude electrons in a different -manner. -

    -

    IMPORTANT NOTE: Whether a section is required depends on how the -molecule template is used by other LAMMPS commands. For example, to -add a molecule via the fix deposit command, the -Coords and Types sections are required. To add a rigid body via the -fix pour command, the Bonds (Angles, etc) sections are -not required, since the molecule will be treated as a rigid body. -Some sections are optional. For example, the fix pour -command can be used to add "molecules" which are clusters of -finite-size granular particles. If the Diameters section is not -specified, each particle in the molecule will have a default diameter -of 1.0. See the doc pages for LAMMPS commands that use molecule -templates for more details. -

    -

    Each section is listed below in alphabetic order. The format of each -section is described including the number of lines it must contain and -rules (if any) for whether it can appear in the data file. In each -case the ID is ignored; it is simply included for readability, and -should be a number from 1 to Nlines for the section, indicating which -atom (or bond, etc) the entry applies to. The lines are assumed to be -listed in order from 1 to Nlines, but LAMMPS does not check for this. -

    -
    - -

    Coords section: -

    -
    • one line per atom -
    • line syntax: ID x y z -
    • x,y,z = coordinate of atom -
    -
    - -

    Types section: -

    -
    • one line per atom -
    • line syntax: ID type -
    • type = atom type of atom -
    -
    - -

    Charges section: -

    -
    • one line per atom -
    • line syntax: ID q -
    • q = charge on atom -
    -

    This section is only allowed for atom styles that -support charge. If this section is not included, the default charge -on each atom in the molecule is 0.0. -

    -
    - -

    Diameters section: -

    -
    • one line per atom -
    • line syntax: ID diam -
    • diam = diameter of atom -
    -

    This section is only allowed for atom styles that -support finite-size spherical particles, e.g. atom_style sphere. If -not listed, the default diameter of each atom in the molecule is 1.0. -

    -
    - -

    Masses section: -

    -
    • one line per atom -
    • line syntax: ID mass -
    • mass = mass of atom -
    -

    This section is only allowed for atom styles that -support per-atom mass, as opposed to per-type mass. See the -mass command for details. If this section is not -included, the default mass for each atom is derived from its volume -(see Diameters section) and a default density of 1.0, in -units of mass/volume. -

    -
    - -

    Bonds section: -

    -
    • one line per bond -
    • line syntax: ID type atom1 atom2 -
    • type = bond type (1-Nbondtype) -
    • atom1,atom2 = IDs of atoms in bond -
    -

    The IDs for the two atoms in each bond should be values -from 1 to Natoms, where Natoms = # of atoms in the molecule. -

    -
    - -

    Angles section: -

    -
    • one line per angle -
    • line syntax: ID type atom1 atom2 atom3 -
    • type = angle type (1-Nangletype) -
    • atom1,atom2,atom3 = IDs of atoms in angle -
    -

    The IDs for the three atoms in each angle should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are -ordered linearly within the angle. Thus the central atom (around -which the angle is computed) is the atom2 in the list. -

    -
    - -

    Dihedrals section: -

    -
    • one line per dihedral -
    • line syntax: ID type atom1 atom2 atom3 atom4 -
    • type = dihedral type (1-Ndihedraltype) -
    • atom1,atom2,atom3,atom4 = IDs of atoms in dihedral -
    -

    The IDs for the four atoms in each dihedral should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are -ordered linearly within the dihedral. -

    -
    - -

    Impropers section: -

    -
    • one line per improper -
    • line syntax: ID type atom1 atom2 atom3 atom4 -
    • type = improper type (1-Nimpropertype) -
    • atom1,atom2,atom3,atom4 = IDs of atoms in improper -
    -

    The IDs for the four atoms in each improper should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The ordering of -the 4 atoms determines the definition of the improper angle used in -the formula for the defined improper style. See -the doc pages for individual styles for details. -

    -
    - -

    Special Bond Counts section: -

    -
    • one line per atom -
    • line syntax: ID N1 N2 N3 -
    • N1 = # of 1-2 bonds -
    • N2 = # of 1-3 bonds -
    • N3 = # of 1-4 bonds -
    -

    N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of -this atom within the topology of the molecule. See the -special_bonds doc page for more discussion of -1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds -section must also appear. If this section is not specied, the -atoms in the molecule will have no special bonds. -

    -
    - -

    Special Bonds section: -

    -
    • one line per atom -
    • line syntax: ID a b c d ... -
    • a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds -
    -

    A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3, -1-4 neighbors of this atom. The IDs should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The first N1 -values should be the 1-2 neighbors, the next N2 should be the 1-3 -neighbors, the last N3 should be the 1-4 neighbors. No atom ID should -appear more than once. See the special_bonds doc -page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section -appears, the Special Bond Counts section must also appear. If this -section is not specied, the atoms in the molecule will have no special -bonds. -

    -
    - -

    Shake Flags section: -

    -
    • one line per atom -
    • line syntax: ID flag -
    • flag = 0,1,2,3,4 -
    -

    This section is only needed when molecules created using the template -will be constrained by SHAKE via the "fix shake" command. The other -two Shake sections must also appear in the file, following this one. -

    -

    The meaning of the flag for each atom is as follows. See the fix -shake doc page for a further description of SHAKE -clusters. -

    -
    • 0 = not part of a SHAKE cluster -
    • 1 = part of a SHAKE angle cluster (two bonds and the angle they form) -
    • 2 = part of a 2-atom SHAKE cluster with a single bond -
    • 3 = part of a 3-atom SHAKE cluster with two bonds -
    • 4 = part of a 4-atom SHAKE cluster with three bonds -
    -
    - -

    Shake Atoms section: -

    -
    • one line per atom -
    • line syntax: ID a b c d -
    • a,b,c,d = IDs of atoms in cluster -
    -

    This section is only needed when molecules created using the template -will be constrained by SHAKE via the "fix shake" command. The other -two Shake sections must also appear in the file. -

    -

    The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms -in the SHAKE cluster that this atom belongs to. The number of values -that must appear is determined by the shake flag for the atom (see the -Shake Flags section above). All atoms in a particular cluster should -list their a,b,c,d values identically. -

    -

    If flag = 0, no a,b,c,d values are listed on the line, just the -(ignored) ID. -

    -

    If flag = 1, a,b,c are listed, where a = ID of central atom in the -angle, and b,c the other two atoms in the angle. -

    -

    If flag = 2, a,b are listed, where a = ID of atom in bond with the the -lowest ID, and b = ID of atom in bond with the highest ID. -

    -

    If flag = 3, a,b,c are listed, where a = ID of central atom, -and b,c = IDs of other two atoms bonded to the central atom. -

    -

    If flag = 4, a,b,c,d are listed, where a = ID of central atom, -and b,c,d = IDs of other three atoms bonded to the central atom. -

    -

    See the fix shake doc page for a further description -of SHAKE clusters. -

    -
    - -

    Shake Bond Types section: -

    -
    • one line per atom -
    • line syntax: ID a b c -
    • a,b,c = bond types (or angle type) of bonds (or angle) in cluster -
    -

    This section is only needed when molecules created using the template -will be constrained by SHAKE via the "fix shake" command. The other -two Shake sections must also appear in the file. -

    -

    The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds -in the SHAKE cluster that this atom belongs to. The number of values -that must appear is determined by the shake flag for the atom (see the -Shake Flags section above). All atoms in a particular cluster should -list their a,b,c values identically. -

    -

    If flag = 0, no a,b,c values are listed on the line, just the -(ignored) ID. -

    -

    If flag = 1, a,b,c are listed, where a = bondtype of the bond between -the central atom and the first non-central atom (value b in the Shake -Atoms section), b = bondtype of the bond between the central atom and -the 2nd non-central atom (value c in the Shake Atoms section), and c = -the angle type (1 to Nangletypes) of the angle between the 3 atoms. -

    -

    If flag = 2, only a is listed, where a = bondtype of the bond between -the 2 atoms in the cluster. -

    -

    If flag = 3, a,b are listed, where a = bondtype of the bond between -the central atom and the first non-central atom (value b in the Shake -Atoms section), and b = bondtype of the bond between the central atom -and the 2nd non-central atom (value c in the Shake Atoms section). -

    -

    If flag = 4, a,b,c are listed, where a = bondtype of the bond between -the central atom and the first non-central atom (value b in the Shake -Atoms section), b = bondtype of the bond between the central atom and -the 2nd non-central atom (value c in the Shake Atoms section), and c = -bondtype of the bond between the central atom and the 3rd non-central -atom (value d in the Shake Atoms section). -

    -

    See the fix shake doc page for a further description -of SHAKE clusters. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    fix deposit, fix pour, -fix_gcmc -

    -

    Default: -

    -

    The default keywords values are offset 0 0 0 0 0 and scale = 1.0. -

    - diff --git a/doc/doc2/neb.html b/doc/doc2/neb.html deleted file mode 100644 index ae2fe0cdbf..0000000000 --- a/doc/doc2/neb.html +++ /dev/null @@ -1,442 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    neb command -

    -

    Syntax: -

    -
    neb etol ftol N1 N2 Nevery file-style arg 
-
    -
    • etol = stopping tolerance for energy (energy units) - -
    • ftol = stopping tolerance for force (force units) - -
    • N1 = max # of iterations (timesteps) to run initial NEB - -
    • N2 = max # of iterations (timesteps) to run barrier-climbing NEB - -
    • Nevery = print replica energies and reaction coordinates every this many timesteps - -
    • file-style= final or each or none - -
        final arg = filename
-    filename = file with initial coords for final replica
-      coords for intermediate replicas are linearly interpolated between first and last replica
-  each arg = filename
-    filename = unique filename for each replica (except first) with its initial coords
-  none arg = no argument
-    all replicas assumed to already have their initial coords 
-
      - -
    -

    Examples: -

    -
    neb 0.1 0.0 1000 500 50 final coords.final
-neb 0.0 0.001 1000 500 50 each coords.initial.$i
-neb 0.0 0.001 1000 500 50 none 
-
    -

    Description: -

    -

    Perform a nudged elastic band (NEB) calculation using multiple -replicas of a system. Two or more replicas must be used; the first -and last are the end points of the transition path. -

    -

    NEB is a method for finding both the atomic configurations and height -of the energy barrier associated with a transition state, e.g. for an -atom to perform a diffusive hop from one energy basin to another in a -coordinated fashion with its neighbors. The implementation in LAMMPS -follows the discussion in these 3 papers: (Henkelman1), -(Henkelman2), and (Nakano). -

    -

    Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the -partition command-line -switch; see Section_start 7 of the -manual. Note that if you have MPI installed, you can run a -multi-replica simulation with more replicas (partitions) than you have -physical processors, e.g you can run a 10-replica simulation on just -one or two processors. You will simply not get the performance -speed-up you would see with one or more physical processors per -replica. See this section of the manual -for further discussion. -

    -

    IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows -there to be one processor per replica. -

    -

    IMPORTANT NOTE: As explained below, a NEB calculation perfoms a damped -dynamics minimization across all the replicas. The mimimizer uses -whatever timestep you have defined in your input script, via the -timestep command. Often NEB will converge more -quickly if you use a timestep about 10x larger than you would normally -use for dynamics simulations. -

    -

    When a NEB calculation is performed, it is assumed that each replica -is running the same system, though LAMMPS does not check for this. -I.e. the simulation domain, the number of atoms, the interaction -potentials, and the starting configuration when the neb command is -issued should be the same for every replica. -

    -

    In a NEB calculation each atom in a replica is connected to the same -atom in adjacent replicas by springs, which induce inter-replica -forces. These forces are imposed by the fix neb -command, which must be used in conjunction with the neb command. The -group used to define the fix neb command defines the NEB atoms which -are the only ones that inter-replica springs are applied to. If the -group does not include all atoms, then non-NEB atoms have no -inter-replica springs and the forces they feel and their motion is -computed in the usual way due only to other atoms within their -replica. Conceptually, the non-NEB atoms provide a background force -field for the NEB atoms. They can be allowed to move during the NEB -minimiation procedure (which will typically induce different -coordinates for non-NEB atoms in different replicas), or held fixed -using other LAMMPS commands such as fix setforce. Note -that the partition command can be used to invoke a -command on a subset of the replicas, e.g. if you wish to hold NEB or -non-NEB atoms fixed in only the end-point replicas. -

    -

    The initial atomic configuration for each of the replicas can be -specified in different manners via the file-style setting, as -discussed below. Only atoms whose initial coordinates should differ -from the current configuration need be specified. -

    -

    Conceptually, the initial configuration for the first replica should -be a state with all the atoms (NEB and non-NEB) having coordinates on -one side of the energy barrier. A perfect energy minimum is not -required, since atoms in the first replica experience no spring forces -from the 2nd replica. Thus the damped dynamics minimizaiton will -drive the first replica to an energy minimum if it is not already -there. However, you will typically get better convergence if the -initial state is already at a minimum. For example, for a system with -a free surface, the surface should be fully relaxed before attempting -a NEB calculation. -

    -

    Likewise, the initial configuration of the final replica should be a -state with all the atoms (NEB and non-NEB) on the other side of the -energy barrier. Again, a perfect energy minimum is not required, -since the atoms in the last replica also experience no spring forces -from the next-to-last replica, and thus the damped dynamics -minimization will drive it to an energy minimum. -

    -

    As explained below, the initial configurations of intermediate -replicas can be atomic coordinates interpolated in a linear fashion -between the first and last replicas. This is often adequate state for -simple transitions. For more complex transitions, it may lead to slow -convergence or even bad results if the minimum energy path (MEP, see -below) of states over the barrier cannot be correctly converged to -from such an initial configuration. In this case, you will want to -generate initial states for the intermediate replicas that are -geometrically closer to the MEP and read them in. -

    -
    - -

    For a file-style setting of final, a filename is specified which -contains atomic coordinates for zero or more atoms, in the format -described below. For each atom that appears in the file, the new -coordinates are assigned to that atom in the final replica. Each -intermediate replica also assigns a new position to that atom in an -interpolated manner. This is done by using the current position of -the atom as the starting point and the read-in position as the final -point. The distance between them is calculated, and the new position -is assigned to be a fraction of the distance. E.g. if there are 10 -replicas, the 2nd replica will assign a position that is 10% of the -distance along a line between the starting and final point, and the -9th replica will assign a position that is 90% of the distance along -the line. Note that this procedure to produce consistent coordinates -across all the replicas, the current coordinates need to be the same -in all replicas. LAMMPS does not check for this, but invalid initial -configurations will likely result if it is not the case. -

    -

    NOTE: The "distance" between the starting and final point is -calculated in a minimum-image sense for a periodic simulation box. -This means that if the two positions are on opposite sides of a box -(periodic in that dimension), the distance between them will be small, -because the periodic image of one of the atoms is close to the other. -Similarly, even if the assigned position resulting from the -interpolation is outside the periodic box, the atom will be wrapped -back into the box when the NEB calculation begins. -

    -

    For a file-style setting of each, a filename is specified which is -assumed to be unique to each replica. This can be done by -using a variable in the filename, e.g. -

    -
    variable i equal part
-neb 0.0 0.001 1000 500 50 each coords.initial.$i 
-
    -

    which in this case will substitute the partition ID (0 to N-1) for the -variable I, which is also effectively the replica ID. See the -variable command for other options, such as using -world-, universe-, or uloop-style variables. -

    -

    Each replica (except the first replica) will read its file, formatted -as described below, and for any atom that appears in the file, assign -the specified coordinates to its atom. The various files do not need -to contain the same set of atoms. -

    -

    For a file-style setting of none, no filename is specified. Each -replica is assumed to already be in its initial configuration at the -time the neb command is issued. This allows each replica to define -its own configuration by reading a replica-specific data or restart or -dump file, via the read_data, -read_restart, or read_dump -commands. The replica-specific names of these files can be specified -as in the discussion above for the each file-style. Also see the -section below for how a NEB calculation can produce restart files, so -that a long calculation can be restarted if needed. -

    -

    IMPORTANT NOTE: None of the file-style settings change the initial -configuration of any atom in the first replica. The first replica -must thus be in the correct initial configuration at the time the neb -command is issued. -

    -
    - -

    A NEB calculation proceeds in two stages, each of which is a -minimization procedure, performed via damped dynamics. To enable -this, you must first define a damped dynamics -min_style, such as quickmin or fire. The cg, -sd, and hftn styles cannot be used, since they perform iterative -line searches in their inner loop, which cannot be easily synchronized -across multiple replicas. -

    -

    The minimizer tolerances for energy and force are set by etol and -ftol, the same as for the minimize command. -

    -

    A non-zero etol means that the NEB calculation will terminate if the -energy criterion is met by every replica. The energies being compared -to etol do not include any contribution from the inter-replica -forces, since these are non-conservative. A non-zero ftol means -that the NEB calculation will terminate if the force criterion is met -by every replica. The forces being compared to ftol include the -inter-replica forces between an atom and its images in adjacent -replicas. -

    -

    The maximum number of iterations in each stage is set by N1 and -N2. These are effectively timestep counts since each iteration of -damped dynamics is like a single timestep in a dynamics -run. During both stages, the potential energy of each -replica and its normalized distance along the reaction path (reaction -coordinate RD) will be printed to the screen and log file every -Nevery timesteps. The RD is 0 and 1 for the first and last replica. -For intermediate replicas, it is the cumulative distance (normalized -by the total cumulative distance) between adjacent replicas, where -"distance" is defined as the length of the 3N-vector of differences in -atomic coordinates, where N is the number of NEB atoms involved in the -transition. These outputs allow you to monitor NEB's progress in -finding a good energy barrier. N1 and N2 must both be multiples -of Nevery. -

    -

    In the first stage of NEB, the set of replicas should converge toward -the minimum energy path (MEP) of conformational states that transition -over the barrier. The MEP for a barrier is defined as a sequence of -3N-dimensional states that cross the barrier at its saddle point, each -of which has a potential energy gradient parallel to the MEP itself. -The replica states will also be roughly equally spaced along the MEP -due to the inter-replica spring force added by the fix -neb command. -

    -

    In the second stage of NEB, the replica with the highest energy -is selected and the inter-replica forces on it are converted to a -force that drives its atom coordinates to the top or saddle point of -the barrier, via the barrier-climbing calculation described in -(Henkelman2). As before, the other replicas rearrange -themselves along the MEP so as to be roughly equally spaced. -

    -

    When both stages are complete, if the NEB calculation was successful, -one of the replicas should be an atomic configuration at the top or -saddle point of the barrier, the potential energies for the set of -replicas should represent the energy profile of the barrier along the -MEP, and the configurations of the replicas should be a sequence of -configurations along the MEP. -

    -
    - -

    A few other settings in your input script are required or advised to -perform a NEB calculation. See the IMPORTANT NOTE about the choice of -timestep at the beginning of this doc page. -

    -

    An atom map must be defined which it is not by default for atom_style -atomic problems. The atom_modify -map command can be used to do this. -

    -

    The "atom_modify sort 0 0.0" command should be used to turn off atom -sorting. -

    -

    NOTE: This sorting restriction will be removed in a future version of -NEB in LAMMPS. -

    -

    The minimizers in LAMMPS operate on all atoms in your system, even -non-NEB atoms, as defined above. To prevent non-NEB atoms from moving -during the minimization, you should use the fix -setforce command to set the force on each of those -atoms to 0.0. This is not required, and may not even be desired in -some cases, but if those atoms move too far (e.g. because the initial -state of your system was not well-minimized), it can cause problems -for the NEB procedure. -

    -

    The damped dynamics minimizers, such as quickmin -and fire), adjust the position and velocity of the atoms via an -Euler integration step. Thus you must define an appropriate -timestep to use with NEB. As mentioned above, NEB -will often converge more quickly if you use a timestep about 10x -larger than you would normally use for dynamics simulations. -

    -
    - -

    Each file read by the neb command containing atomic coordinates used -to initialize one or more replicas must be formatted as follows. -

    -

    The file can be ASCII text or a gzipped text file (detected by a .gz -suffix). The file can contain initial blank lines or comment lines -starting with "#" which are ignored. The first non-blank, non-comment -line should list N = the number of lines to follow. The N successive -lines contain the following information: -

    -
    ID1 x1 y1 z1
-ID2 x2 y2 z2
-...
-IDN xN yN zN 
-
    -

    The fields are the the atom ID, followed by the x,y,z coordinates. -The lines can be listed in any order. Additional trailing information -on the line is OK, such as a comment. -

    -

    Note that for a typical NEB calculation you do not need to specify -initial coordinates for very many atoms to produce differing starting -and final replicas whose intermediate replicas will converge to the -energy barrier. Typically only new coordinates for atoms -geometrically near the barrier need be specified. -

    -

    Also note there is no requirement that the atoms in the file -correspond to the NEB atoms in the group defined by the fix -neb command. Not every NEB atom need be in the file, -and non-NEB atoms can be listed in the file. -

    -
    - -

    Four kinds of output can be generated during a NEB calculation: energy -barrier statistics, thermodynamic output by each replica, dump files, -and restart files. -

    -

    When running with multiple partitions (each of which is a replica in -this case), the print-out to the screen and master log.lammps file -contains a line of output, printed once every Nevery timesteps. It -contains the timestep, the maximum force per replica, the maximum -force per atom (in any replica), potential gradients in the initial, - final, and climbing replicas, -the forward and backward energy barriers, -the total reaction coordinate (RDT), and -the normalized reaction coordinate and potential energy of each replica. -

    -

    The "maximum force per replica" is -the two-norm of the 3N-length force vector for the atoms in each -replica, maximized across replicas, which is what the ftol setting -is checking against. In this case, N is all the atoms in each -replica. The "maximum force per atom" is the maximum force component -of any atom in any replica. The potential gradients are the two-norm -of the 3N-length force vector solely due to the interaction potential i.e. -without adding in inter-replica forces. Note that inter-replica forces -are zero in the initial and final replicas, and only affect -the direction in the climbing replica. For this reason, the "maximum -force per replica" is often equal to the potential gradient in the -climbing replica. In the first stage of NEB, there is no climbing -replica, and so the potential gradient in the highest energy replica -is reported, since this replica will become the climbing replica -in the second stage of NEB. -

    -

    The "reaction coordinate" (RD) for each -replica is the two-norm of the 3N-length vector of distances between -its atoms and the preceding replica's atoms, added to the RD of the -preceding replica. The RD of the first replica RD1 = 0.0; -the RD of the final replica RDN = RDT, the total reaction coordinate. -The normalized RDs are divided by RDT, -so that they form a monotonically increasing sequence -from zero to one. When computing RD, N only includes the atoms -being operated on by the fix neb command. -

    -

    The forward (reverse) energy barrier is the potential energy of the highest -replica minus the energy of the first (last) replica. -

    -

    When running on multiple partitions, LAMMPS produces additional log -files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a -NEB calculation, these contain the thermodynamic output for each -replica. -

    -

    If dump commands in the input script define a filename -that includes a universe or uloop style variable, -then one dump file (per dump command) will be created for each -replica. At the end of the NEB calculation, the final snapshot in -each file will contain the sequence of snapshots that transition the -system over the energy barrier. Earlier snapshots will show the -convergence of the replicas to the MEP. -

    -

    Likewise, restart filenames can be specified with a -universe or uloop style variable, to generate -restart files for each replica. These may be useful if the NEB -calculation fails to converge properly to the MEP, and you wish to -restart the calculation from an intermediate point with altered -parameters. -

    -

    There are 2 Python scripts provided in the tools/python directory, -neb_combine.py and neb_final.py, which are useful in analyzing output -from a NEB calculation. Assume a NEB simulation with M replicas, and -the NEB atoms labelled with a specific atom type. -

    -

    The neb_combine.py script extracts atom coords for the NEB atoms from -all M dump files and creates a single dump file where each snapshot -contains the NEB atoms from all the replicas and one copy of non-NEB -atoms from the first replica (presumed to be identical in other -replicas). This can be visualized/animated to see how the NEB atoms -relax as the NEB calculation proceeds. -

    -

    The neb_final.py script extracts the final snapshot from each of the M -dump files to create a single dump file with M snapshots. This can be -visualized to watch the system make its transition over the energy -barrier. -

    -

    To illustrate, here are images from the final snapshot produced by the -neb_combine.py script run on the dump files produced by the two -example input scripts in examples/neb. Click on them to see a larger -image. -

    - - - - -
    - -

    Restrictions: -

    -

    This command can only be used if LAMMPS was built with the REPLICA -package. See the Making LAMMPS section -for more info on packages. -

    -

    Related commands: -

    -

    prd, temper, fix -langevin, fix viscous -

    -

    Default: none -

    -
    - - - -

    (Henkelman1) Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). -

    - - -

    (Henkelman2) Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, -9901-9904 (2000). -

    - - -

    (Nakano) Nakano, Comp Phys Comm, 178, 280-289 (2008). -

    - diff --git a/doc/doc2/neigh_modify.html b/doc/doc2/neigh_modify.html deleted file mode 100644 index 38e8f15f64..0000000000 --- a/doc/doc2/neigh_modify.html +++ /dev/null @@ -1,219 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    neigh_modify command -

    -

    Syntax: -

    -
    neigh_modify keyword values ... 
-
    -
    • one or more keyword/value pairs may be listed - -
      keyword = delay or every or check or once or cluster or include or exclude or page or one or binsize
-  delay value = N
-    N = delay building until this many steps since last build
-  every value = M
-    M = build neighbor list every this many steps
-  check value = yes or no
-    yes = only build if some atom has moved half the skin distance or more
-    no = always build on 1st step that every and delay are satisfied
-  once
-    yes = only build neighbor list once at start of run and never rebuild
-    no = rebuild neighbor list according to other settings
-  cluster
-    yes = check bond,angle,etc neighbor list for nearby clusters
-    no = do not check bond,angle,etc neighbor list for nearby clusters
-  include value = group-ID
-    group-ID = only build pair neighbor lists for atoms in this group
-  exclude values:
-    type M N
-      M,N = exclude if one atom in pair is type M, other is type N
-    group group1-ID group2-ID
-      group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
-    molecule group-ID
-      groupname = exclude if both atoms are in the same molecule and in the same group
-    none
-      delete all exclude settings
-  page value = N
-    N = number of pairs stored in a single neighbor page
-  one value = N
-    N = max number of neighbors of one atom
-  binsize value = size
-    size = bin size for neighbor list construction (distance units) 
-
      - -
    -

    Examples: -

    -
    neigh_modify every 2 delay 10 check yes page 100000
-neigh_modify exclude type 2 3
-neigh_modify exclude group frozen frozen check no
-neigh_modify exclude group residue1 chain3
-neigh_modify exclude molecule rigid 
-
    -

    Description: -

    -

    This command sets parameters that affect the building and use of -pairwise neighbor lists. Depending on what pair interactions and -other commands are defined, a simulation may require one or more -neighbor lists. -

    -

    The every, delay, check, and once options affect how often -lists are built as a simulation runs. The delay setting means never -build new lists until at least N steps after the previous build. The -every setting means build lists every M steps (after the delay has -passed). If the check setting is no, the lists are built on the -first step that satisfies the delay and every settings. If the -check setting is yes, then the every and delay settings -determine when a build may possibly be performed, but an actual build -only occurs if some atom has moved more than half the skin distance -(specified in the neighbor command) since the last -build. -

    -

    If the once setting is yes, then the neighbor list is only built -once at the beginning of each run, and never rebuilt, except on steps -when a restart file is written, or steps when a fix forces a rebuild -to occur (e.g. fixes that create or delete atoms, such as fix -deposit or fix evaporate). -This setting should only be made if you are certain atoms will not -move far enough that the neighbor list should be rebuilt, e.g. running -a simulation of a cold crystal. Note that it is not that expensive to -check if neighbor lists should be rebuilt. -

    -

    When the rRESPA integrator is used (see the run_style -command), the every and delay parameters refer to the longest -(outermost) timestep. -

    -

    The cluster option does a sanity test every time neighbor lists are -built for bond, angle, dihedral, and improper interactions, to check -that each set of 2, 3, or 4 atoms is a cluster of nearby atoms. It -does this by computing the distance between pairs of atoms in the -interaction and insuring they are not further apart than half the -periodic box length. If they are, an error is generated, since the -interaction would be computed between far-away atoms instead of their -nearby periodic images. The only way this should happen is if the -pairwise cutoff is so short that atoms that are part of the same -interaction are not communicated as ghost atoms. This is an unusual -model (e.g. no pair interactions at all) and the problem can be fixed -by use of the comm_modify cutoff command. Note -that to save time, the default cluster setting is no, so that this -check is not performed. -

    -

    The include option limits the building of pairwise neighbor lists to -atoms in the specified group. This can be useful for models where a -large portion of the simulation is particles that do not interact with -other particles or with each other via pairwise interactions. The -group specified with this option must also be specified via the -atom_modify first command. -

    -

    The exclude option turns off pairwise interactions between certain -pairs of atoms, by not including them in the neighbor list. These are -sample scenarios where this is useful: -

    -
    • In crack simulations, pairwise interactions can be shut off between 2 -slabs of atoms to effectively create a crack. - -
    • When a large collection of atoms is treated as frozen, interactions -between those atoms can be turned off to save needless -computation. E.g. Using the fix setforce command -to freeze a wall or portion of a bio-molecule. - -
    • When one or more rigid bodies are specified, interactions within each -body can be turned off to save needless computation. See the fix -rigid command for more details. -
    -

    The exclude type option turns off the pairwise interaction if one -atom is of type M and the other of type N. M can equal N. The -exclude group option turns off the interaction if one atom is in the -first group and the other is the second. Group1-ID can equal -group2-ID. The exclude molecule option turns off the interaction if -both atoms are in the specified group and in the same molecule, as -determined by their molecule ID. -

    -

    Each of the exclude options can be specified multiple times. The -exclude type option is the most efficient option to use; it requires -only a single check, no matter how many times it has been specified. -The other exclude options are more expensive if specified multiple -times; they require one check for each time they have been specified. -

    -

    Note that the exclude options only affect pairwise interactions; see -the delete_bonds command for information on -turning off bond interactions. -

    -

    IMPORTANT NOTE: Excluding pairwise interactions will not work -correctly when also using a long-range solver via the -kspace_style command. LAMMPS will give a warning -to this effect. This is because the short-range pairwise interaction -needs to subtract off a term from the total energy for pairs whose -short-range interaction is excluded, to compensate for how the -long-range solver treats the interaction. This is done correctly for -pairwise interactions that are excluded (or weighted) via the -special_bonds command. But it is not done for -interactions that are excluded via these neigh_modify exclude options. -

    -

    The page and one options affect how memory is allocated for the -neighbor lists. For most simulations the default settings for these -options are fine, but if a very large problem is being run or a very -long cutoff is being used, these parameters can be tuned. The indices -of neighboring atoms are stored in "pages", which are allocated one -after another as they fill up. The size of each page is set by the -page value. A new page is allocated when the next atom's neighbors -could potentially overflow the list. This threshold is set by the -one value which tells LAMMPS the maximum number of neighbor's one -atom can have. -

    -

    IMPORTANT NOTE: LAMMPS can crash without an error message if the -number of neighbors for a single particle is larger than the page -setting, which means it is much, much larger than the one setting. -This is because LAMMPS doesn't error check these limits for every -pairwise interaction (too costly), but only after all the particle's -neighbors have been found. This problem usually means something is -very wrong with the way you've setup your problem (particle spacing, -cutoff length, neighbor skin distance, etc). If you really expect -that many neighbors per particle, then boost the one and page -settings accordingly. -

    -

    The binsize option allows you to specify what size of bins will be -used in neighbor list construction to sort and find neighboring atoms. -By default, for neighbor style bin, LAMMPS uses bins -that are 1/2 the size of the maximum pair cutoff. For neighbor style -multi, the bins are 1/2 the size of the minimum pair -cutoff. Typically these are good values values for minimizing the -time for neighbor list construction. This setting overrides the -default. If you make it too big, there is little overhead due to -looping over bins, but more atoms are checked. If you make it too -small, the optimal number of atoms is checked, but bin overhead goes -up. If you set the binsize to 0.0, LAMMPS will use the default -binsize of 1/2 the cutoff. -

    -

    Restrictions: -

    -

    If the "delay" setting is non-zero, then it must be a multiple of the -"every" setting. -

    -

    The exclude molecule option can only be used with atom styles that -define molecule IDs. -

    -

    The value of the page setting must be at least 10x larger than the -one setting. This insures neighbor pages are not mostly empty -space. -

    -

    Related commands: -

    -

    neighbor, delete_bonds -

    -

    Default: -

    -

    The option defaults are delay = 10, every = 1, check = yes, once = no, -cluster = no, include = all, exclude = none, page = 100000, one = -2000, and binsize = 0.0. -

    - diff --git a/doc/doc2/neighbor.html b/doc/doc2/neighbor.html deleted file mode 100644 index 9618531ee0..0000000000 --- a/doc/doc2/neighbor.html +++ /dev/null @@ -1,88 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    neighbor command -

    -

    Syntax: -

    -
    neighbor skin style 
-
    -
    • skin = extra distance beyond force cutoff (distance units) -
    • style = bin or nsq or multi -
    -

    Examples: -

    -
    neighbor 0.3 bin
-neighbor 2.0 nsq 
-
    -

    Description: -

    -

    This command sets parameters that affect the building of pairwise -neighbor lists. All atom pairs within a neighbor cutoff distance -equal to the their force cutoff plus the skin distance are stored in -the list. Typically, the larger the skin distance, the less often -neighbor lists need to be built, but more pairs must be checked for -possible force interactions every timestep. The default value for -skin depends on the choice of units for the simulation; see the -default values below. -

    -

    The skin distance is also used to determine how often atoms migrate -to new processors if the check option of the -neigh_modify command is set to yes. Atoms are -migrated (communicated) to new processors on the same timestep that -neighbor lists are re-built. -

    -

    The style value selects what algorithm is used to build the list. -The bin style creates the list by binning which is an operation that -scales linearly with N/P, the number of atoms per processor where N = -total number of atoms and P = number of processors. It is almost -always faster than the nsq style which scales as (N/P)^2. For -unsolvated small molecules in a non-periodic box, the nsq choice can -sometimes be faster. Either style should give the same answers. -

    -

    The multi style is a modified binning algorithm that is useful for -systems with a wide range of cutoff distances, e.g. due to different -size particles. For the bin style, the bin size is set to 1/2 of -the largest cutoff distance between any pair of atom types and a -single set of bins is defined to search over for all atom types. This -can be inefficient if one pair of types has a very long cutoff, but -other type pairs have a much shorter cutoff. For style multi the -bin size is set to 1/2 of the shortest cutoff distance and multiple -sets of bins are defined to search over for different atom types. -This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. See the comm_modify -mode multi command for a communication option option -that may also be beneficial for simulations of this kind. -

    -

    The neigh_modify command has additional options -that control how often neighbor lists are built and which pairs are -stored in the list. -

    -

    When a run is finished, counts of the number of neighbors stored in -the pairwise list and the number of times neighbor lists were built -are printed to the screen and log file. See this -section for details. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    neigh_modify, units, -comm_modify -

    -

    Default: -

    -0.3 bin for units = lj, skin = 0.3 sigma
    -2.0 bin for units = real or metal, skin = 2.0 Angstroms
    -0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
    -0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm
    - - diff --git a/doc/doc2/newton.html b/doc/doc2/newton.html deleted file mode 100644 index 94e20608e6..0000000000 --- a/doc/doc2/newton.html +++ /dev/null @@ -1,67 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    newton command -

    -

    Syntax: -

    -
    newton flag
-newton flag1 flag2 
-
    -
    • flag = on or off for both pairwise and bonded interactions -
    • flag1 = on or off for pairwise interactions -
    • flag2 = on or off for bonded interactions -
    -

    Examples: -

    -
    newton off
-newton on off 
-
    -

    Description: -

    -

    This command turns Newton's 3rd law on or off for pairwise and -bonded interactions. For most problems, setting Newton's 3rd law to -on means a modest savings in computation at the cost of two times -more communication. Whether this is faster depends on problem size, -force cutoff lengths, a machine's compute/communication ratio, and how -many processors are being used. -

    -

    Setting the pairwise newton flag to off means that if two -interacting atoms are on different processors, both processors compute -their interaction and the resulting force information is not -communicated. Similarly, for bonded interactions, newton off means -that if a bond, angle, dihedral, or improper interaction contains -atoms on 2 or more processors, the interaction is computed by each -processor. -

    -

    LAMMPS should produce the same answers for any newton flag settings, -except for round-off issues. -

    -

    With run_style respa and only bonded interactions -(bond, angle, etc) computed in the innermost timestep, it may be -faster to turn newton off for bonded interactions, to avoid extra -communication in the innermost loop. -

    -

    Restrictions: -

    -

    The newton bond setting cannot be changed after the simulation box is -defined by a read_data or -create_box command. -

    -

    Related commands: -

    -

    run_style respa -

    -

    Default: -

    -
    newton on 
-
    - diff --git a/doc/doc2/next.html b/doc/doc2/next.html deleted file mode 100644 index ed8effb539..0000000000 --- a/doc/doc2/next.html +++ /dev/null @@ -1,148 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    next command -

    -

    Syntax: -

    -
    next variables 
-
    -
    • variables = one or more variable names -
    -

    Examples: -

    -
    next x
-next a t x myTemp 
-
    -

    Description: -

    -

    This command is used with variables defined by the -variable command. It assigns the next value to the -variable from the list of values defined for that variable by the -variable command. Thus when that variable is -subsequently substituted for in an input script command, the new value -is used. -

    -

    See the variable command for info on how to define and -use different kinds of variables in LAMMPS input scripts. If a -variable name is a single lower-case character from "a" to "z", it can -be used in an input script command as $a or $z. If it is multiple -letters, it can be used as ${myTemp}. -

    -

    If multiple variables are used as arguments to the next command, -then all must be of the same variable style: index, loop, file, -universe, or uloop. An exception is that universe- and -uloop-style variables can be mixed in the same next command. -

    -

    All the variables specified with the next command are incremented by -one value from their respective list of values. A file-style -variable reads the next line from its associated file. An -atomfile-style variable reads the next set of lines (one per atom) -from its associated file. String- or atom- or equal- or -world-style variables cannot be used with the the next command, -since they only store a single value. -

    -

    When any of the variables in the next command has no more values, a -flag is set that causes the input script to skip the next -jump command encountered. This enables a loop containing -a next command to exit. As explained in the variable -command, the variable that has exhausted its values is also deleted. -This allows it to be used and re-defined later in the input script. -File-style and atomfile-style variables are exhausted when the -end-of-file is reached. -

    -

    When the next command is used with index- or loop-style variables, -the next value is assigned to the variable for all processors. When -the next command is used with file-style variables, the next line is -read from its file and the string assigned to the variable. When the -next command is used with atomfile-style variables, the next set of -per-atom values is read from its file and assigned to the variable. -

    -

    When the next command is used with universe- or uloop-style -variables, all universe- or uloop-style variables must be listed -in the next command. This is because of the manner in which the -incrementing is done, using a single lock file for all variables. The -next value (for each variable) is assigned to whichever processor -partition executes the command first. All processors in the partition -are assigned the same value(s). Running LAMMPS on multiple partitions -of processors via the "-partition" command-line switch is described in -this section of the manual. Universe- -and uloop-style variables are incremented using the files -"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will -see in your directory during and after such a LAMMPS run. -

    -

    Here is an example of running a series of simulations using the next -command with an index-style variable. If this input script is named -in.polymer, 8 simulations would be run using data files from -directories run1 thru run8. -

    -
    variable d index run1 run2 run3 run4 run5 run6 run7 run8
-shell cd $d
-read_data data.polymer
-run 10000
-shell cd ..
-clear
-next d
-jump in.polymer 
-
    -

    If the variable "d" were of style universe, and the same in.polymer -input script were run on 3 partitions of processors, then the first 3 -simulations would begin, one on each set of processors. Whichever -partition finished first, it would assign variable "d" the 4th value -and run another simulation, and so forth until all 8 simulations were -finished. -

    -

    Jump and next commands can also be nested to enable multi-level loops. -For example, this script will run 15 simulations in a double loop. -

    -
    variable i loop 3
-  variable j loop 5
-  clear
-  ...
-  read_data data.polymer.$i$j
-  print Running simulation $i.$j
-  run 10000
-  next j
-  jump in.script
-next i
-jump in.script 
-
    -

    Here is an example of a double loop which uses the if and -jump commands to break out of the inner loop when a -condition is met, then continues iterating thru the outer loop. -

    -
    label	    loopa
-variable    a loop 5
-  label	    loopb
-  variable  b loop 5
-  print	    "A,B = $a,$b"
-  run       10000
-  if	    $b > 2 then "jump in.script break"
-  next	    b
-  jump	    in.script loopb
-label	    break
-variable    b delete 
-
    -
    next	    a
-jump	    in.script loopa 
-
    -

    Restrictions: -

    -

    As described above. -

    -

    Related commands: -

    -

    jump, include, shell, -variable, -

    -

    Default: none -

    - diff --git a/doc/doc2/package.html b/doc/doc2/package.html deleted file mode 100644 index 21f3bbb349..0000000000 --- a/doc/doc2/package.html +++ /dev/null @@ -1,675 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    package command -

    -

    Syntax: -

    -
    package style args 
-
    -
    • style = cuda or gpu or intel or kokkos or omp - -
    • args = arguments specific to the style - -
        cuda args = Ngpu keyword value ...
-    Ngpu = # of GPUs per node
-    zero or more keyword/value pairs may be appended
-    keywords = newton or gpuID or timing or test or thread
-      newton = off or on
-        off = set Newton pairwise and bonded flags off (default)
-        on = set Newton pairwise and bonded flags on
-      gpuID values = gpu1 .. gpuN
-        gpu1 .. gpuN = IDs of the Ngpu GPUs to use
-      timing values = none
-      test values = id
-        id = atom-ID of a test particle
-      thread = auto or tpa or bpa
-        auto = test whether tpa or bpa is faster
-        tpa = one thread per atom
-        bpa = one block per atom
-  gpu args = Ngpu keyword value ...
-    Ngpu = # of GPUs per node
-    zero or more keyword/value pairs may be appended 
-    keywords = neigh or newton or binsize or split or gpuID or tpa or device or blocksize
-      neigh value = yes or no
-        yes = neighbor list build on GPU (default)
-        no = neighbor list build on CPU
-      newton = off or on
-        off = set Newton pairwise flag off (default and required)
-        on = set Newton pairwise flag on (currently not allowed)
-      binsize value = size
-        size = bin size for neighbor list construction (distance units)
-      split = fraction
-        fraction = fraction of atoms assigned to GPU (default = 1.0)
-      gpuID values = first last
-        first = ID of first GPU to be used on each node
-        last = ID of last GPU to be used on each node
-      tpa value = Nthreads
-        Nthreads = # of GPU threads used per atom
-      device value = device_type
-        device_type = kepler or fermi or cypress or generic
-      blocksize value = size
-        size = thread block size for pair force computation
-  intel args = NPhi keyword value ...
-    Nphi = # of coprocessors per node
-    zero or more keyword/value pairs may be appended 
-    keywords = omp or mode or balance or ghost or tpc or tptask or no_affinity
-      omp value = Nthreads
-        Nthreads = number of OpenMP threads to use on CPU (default = 0)
-      mode value = single or mixed or double
-        single = perform force calculations in single precision
-        mixed = perform force calculations in mixed precision
-        double = perform force calculations in double precision
-      balance value = split
-        split = fraction of work to offload to coprocessor, -1 for dynamic
-      ghost value = yes or no
-        yes = include ghost atoms for offload
-        no = do not include ghost atoms for offload
-      tpc value = Ntpc
-        Ntpc = max number of coprocessor threads per coprocessor core (default = 4)
-      tptask value = Ntptask
-        Ntptask = max number of coprocessor threads per MPI task (default = 240)
-      no_affinity values = none
-  kokkos args = keyword value ...
-    zero or more keyword/value pairs may be appended
-    keywords = neigh or newton or binsize or comm or comm/exchange or comm/forward
-      neigh value = full or half/thread or half or n2 or full/cluster
-        full = full neighbor list
-        half/thread = half neighbor list built in thread-safe manner
-        half = half neighbor list, not thread-safe, only use when 1 thread/MPI task
-        n2 = non-binning neighbor list build, O(N^2) algorithm
-        full/cluster = full neighbor list with clustered groups of atoms
-      newton = off or on
-        off = set Newton pairwise and bonded flags off (default)
-        on = set Newton pairwise and bonded flags on
-      binsize value = size
-        size = bin size for neighbor list construction (distance units)
-      comm value = no or host or device
-        use value for both comm/exchange and comm/forward
-      comm/exchange value = no or host or device
-      comm/forward value = no or host or device
-        no = perform communication pack/unpack in non-KOKKOS mode
-        host = perform pack/unpack on host (e.g. with OpenMP threading)
-        device = perform pack/unpack on device (e.g. on GPU)
-  omp args = Nthreads keyword value ...
-    Nthread = # of OpenMP threads to associate with each MPI process
-    zero or more keyword/value pairs may be appended 
-    keywords = neigh
-      neigh value = yes or no
-        yes = threaded neighbor list build (default)
-        no = non-threaded neighbor list build 
-
      - -
    -

    Examples: -

    -
    package gpu 1
-package gpu 1 split 0.75
-package gpu 2 split -1.0
-package cuda 2 gpuID 0 2
-package cuda 1 test 3948
-package kokkos neigh half/thread comm device
-package omp 0 neigh no
-package omp 4
-package intel 1
-package intel 2 omp 4 mode mixed balance 0.5 
-
    -

    Description: -

    -

    This command invokes package-specific settings for the various -accelerator packages available in LAMMPS. Currently the following -packages use settings from this command: USER-CUDA, GPU, USER-INTEL, -KOKKOS, and USER-OMP. -

    -

    If this command is specified in an input script, it must be near the -top of the script, before the simulation box has been defined. This -is because it specifies settings that the accelerator packages use in -their intialization, before a simultion is defined. -

    -

    This command can also be specified from the command-line when -launching LAMMPS, using the "-pk" command-line -switch. The syntax is exactly the same as -when used in an input script. -

    -

    Note that all of the accelerator packages require the package command -to be specified (except the OPT package), if the package is to be used -in a simulation (LAMMPS can be built with an accelerator package -without using it in a particular simulation). However, in all cases, -a default version of the command is typically invoked by other -accelerator settings. -

    -

    The USER-CUDA and KOKKOS packages require a "-c on" or "-k on" -command-line switch respectively, which -invokes a "package cuda" or "package kokkos" command with default -settings. -

    -

    For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf -intel" or "-sf omp" command-line switch -is used to auto-append accelerator suffixes to various styles in the -input script, then those switches also invoke a "package gpu", -"package intel", or "package omp" command with default settings. -

    -

    IMPORTANT NOTE: A package command for a particular style can be -invoked multiple times when a simulation is setup, e.g. by the "-c -on", "-k on", "-sf", and "-pk" command-line -switches, and by using this command in an -input script. Each time it is used all of the style options are set, -either to default values or to specified settings. I.e. settings from -previous invocations do not persist across multiple invocations. -

    -

    See the Section Accelerate section of the -manual for more details about using the various accelerator packages -for speeding up LAMMPS simulations. -

    -
    - -

    The cuda style invokes settings associated with the use of the -USER-CUDA package. -

    -

    The Ngpus argument sets the number of GPUs per node. There must be -exactly one MPI task per GPU, as set by the mpirun or mpiexec command. -

    -

    Optional keyword/value pairs can also be specified. Each has a -default value as listed below. -

    -

    The newton keyword sets the Newton flags for pairwise and bonded -interactions to off or on, the same as the newton -command allows. The default is off because this will almost always -give better performance for the USER-CUDA package. This means -more computation is done, but less communication. -

    -

    The gpuID keyword allows selection of which GPUs on each node will -be used for a simulation. GPU IDs range from 0 to N-1 where N is the -physical number of GPUs/node. An ID is specified for each of the -Ngpus being used. For example if you have three GPUs on a machine, -one of which is used for the X-Server (the GPU with the ID 1) while -the others (with IDs 0 and 2) are used for computations you would -specify: -

    -
    package cuda 2 gpuID 0 2 
-
    -

    The purpose of the gpuID keyword is to allow two (or more) -simulations to be run on one workstation. In that case one could set -the first simulation to use GPU 0 and the second to use GPU 1. This is -not necessary however, if the GPUs are in what is called compute -exclusive mode. Using that setting, every process will get its own -GPU automatically. This compute exclusive mode can be set as root -using the nvidia-smi tool which is part of the CUDA installation. -

    -

    Also note that if the gpuID keyword is not used, the USER-CUDA -package sorts existing GPUs on each node according to their number of -multiprocessors. This way, compute GPUs will be priorized over -X-Server GPUs. -

    -

    If the timing keyword is specified, detailed timing information for -various subroutines will be output. -

    -

    If the test keyword is specified, information for the specified atom -with atom-ID will be output at several points during each timestep. -This is mainly usefull for debugging purposes. Note that the -simulation slow down dramatically if this option is used. -

    -

    The thread keyword can be used to specify how GPU threads are -assigned work during pair style force evaluation. If the value = -tpa, one thread per atom is used. If the value = bpa, one block -per atom is used. If the value = auto, a short test is performed at -the beginning of each run to determing where tpa or bpa mode is -faster. The result of this test is output. Since auto is the -default value, it is usually not necessary to use this keyword. -

    -
    - -

    The gpu style invokes settings associated with the use of the GPU -package. -

    -

    The Ngpu argument sets the number of GPUs per node. There must be -at least as many MPI tasks per node as GPUs, as set by the mpirun or -mpiexec command. If there are more MPI tasks (per node) -than GPUs, multiple MPI tasks will share each GPU. -

    -

    Optional keyword/value pairs can also be specified. Each has a -default value as listed below. -

    -

    The neigh keyword specifies where neighbor lists for pair style -computation will be built. If neigh is yes, which is the default, -neighbor list building is performed on the GPU. If neigh is no, -neighbor list building is performed on the CPU. GPU neighbor list -building currently cannot be used with a triclinic box. GPU neighbor -list calculation currently cannot be used with -hybrid pair styles. GPU neighbor lists are not -compatible with comannds that are not GPU-enabled. When a non-GPU -enabled command requires a neighbor list, it will also be built on the -CPU. In these cases, it will typically be more efficient to only use -CPU neighbor list builds. -

    -

    The newton keyword sets the Newton flags for pairwise (not bonded) -interactions to off or on, the same as the newton -command allows. Currently, only an off value is allowed, since all -the GPU package pair styles require this setting. This means more -computation is done, but less communication. In the future a value of -on may be allowed, so the newton keyword is included as an option -for compatibility with the package command for other accelerator -styles. Note that the newton setting for bonded interactions is not -affected by this keyword. -

    -

    The binsize keyword sets the size of bins used to bin atoms in -neighbor list builds performed on the GPU, if neigh = yes is set. -If binsize is set to 0.0 (the default), then bins = the size of the -pairwise cutoff + neighbor skin distance. This is 2x larger than the -LAMMPS default used for neighbor list building on the CPU. This will -be close to optimal for the GPU, so you do not normally need to use -this keyword. Note that if you use a longer-than-usual pairwise -cutoff, e.g. to allow for a smaller fraction of KSpace work with a -long-range Coulombic solver because the GPU is -faster at performing pairwise interactions, then it may be optimal to -make the binsize smaller than the default. For example, with a -cutoff of 20*sigma in LJ units and a neighbor skin -distance of sigma, a binsize = 5.25*sigma can be more efficient than -the default. -

    -

    The split keyword can be used for load balancing force calculations -between CPU and GPU cores in GPU-enabled pair styles. If 0 < split < -1.0, a fixed fraction of particles is offloaded to the GPU while force -calculation for the other particles occurs simulataneously on the CPU. -If split < 0.0, the optimal fraction (based on CPU and GPU timings) -is calculated every 25 timesteps, i.e. dynamic load-balancing across -the CPU and GPU is performed. If split = 1.0, all force -calculations for GPU accelerated pair styles are performed on the GPU. -In this case, other hybrid pair interactions, -bond, angle, -dihedral, improper, and -long-range calculations can be performed on the -CPU while the GPU is performing force calculations for the GPU-enabled -pair style. If all CPU force computations complete before the GPU -completes, LAMMPS will block until the GPU has finished before -continuing the timestep. -

    -

    As an example, if you have two GPUs per node and 8 CPU cores per node, -and would like to run on 4 nodes (32 cores) with dynamic balancing of -force calculation across CPU and GPU cores, you could specify -

    -
    mpirun -np 32 -sf gpu -in in.script    # launch command
-package gpu 2 split -1                 # input script command 
-
    -

    In this case, all CPU cores and GPU devices on the nodes would be -utilized. Each GPU device would be shared by 4 CPU cores. The CPU -cores would perform force calculations for some fraction of the -particles at the same time the GPUs performed force calculation for -the other particles. -

    -

    The gpuID keyword allows selection of which GPUs on each node will -be used for a simulation. The first and last values specify the -GPU IDs to use (from 0 to Ngpu-1). By default, first = 0 and last = -Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number -of physical GPUs. If you only wish to use a subset, set Ngpu to a -smaller number and first/last to a sub-range of the available GPUs. -

    -

    The tpa keyword sets the number of GPU thread per atom used to -perform force calculations. With a default value of 1, the number of -threads will be chosen based on the pair style, however, the value can -be set explicitly with this keyword to fine-tune performance. For -large cutoffs or with a small number of particles per GPU, increasing -the value can improve performance. The number of threads per atom must -be a power of 2 and currently cannot be greater than 32. -

    -

    The device keyword can be used to tune parameters optimized for a -specific accelerator, when using OpenCL. For CUDA, the device -keyword is ignored. Currently, the device type is limited to NVIDIA -Kepler, NVIDIA Fermi, AMD Cypress, or a generic device. More devices -may be added later. The default device type can be specified when -building LAMMPS with the GPU library, via settings in the -lib/gpu/Makefile that is used. -

    -

    The blocksize keyword allows you to tweak the number of threads used -per thread block. This number should be a multiple of 32 (for GPUs) -and its maximum depends on the specific GPU hardware. Typical choices -are 64, 128, or 256. A larger blocksize increases occupancy of -individual GPU cores, but reduces the total number of thread blocks, -thus may lead to load imbalance. -

    -
    - -

    The intel style invokes settings associated with the use of the -USER-INTEL package. All of its settings, except the omp and mode -keywords, are ignored if LAMMPS was not built with Xeon Phi -coprocessor support. All of its settings, including the omp and -mode keyword are applicable if LAMMPS was built with coprocessor -support. -

    -

    The Nphi argument sets the number of coprocessors per node. -This can be set to any value, including 0, if LAMMPS was not -built with coprocessor support. -

    -

    Optional keyword/value pairs can also be specified. Each has a -default value as listed below. -

    -

    The omp keyword determines the number of OpenMP threads allocated -for each MPI task when any portion of the interactions computed by a -USER-INTEL pair style are run on the CPU. This can be the case even -if LAMMPS was built with coprocessor support; see the balance -keyword discussion below. If you are running with less MPI tasks/node -than there are CPUs, it can be advantageous to use OpenMP threading on -the CPUs. -

    -

    IMPORTANT NOTE: The omp keyword has nothing to do with coprocessor -threads on the Xeon Phi; see the tpc and tptask keywords below for -a discussion of coprocessor threads. -

    -

    The Nthread value for the omp keyword sets the number of OpenMP -threads allocated for each MPI task. Setting Nthread = 0 (the -default) instructs LAMMPS to use whatever value is the default for the -given OpenMP environment. This is usually determined via the -OMP_NUM_THREADS environment variable or the compiler runtime, which -is usually a value of 1. -

    -

    For more details, including examples of how to set the OMP_NUM_THREADS -environment variable, see the discussion of the Nthreads setting on -this doc page for the "package omp" command. Nthreads is a required -argument for the USER-OMP package. Its meaning is exactly the same -for the USER-INTEL pacakge. -

    -

    IMPORTANT NOTE: If you build LAMMPS with both the USER-INTEL and -USER-OMP packages, be aware that both packages allow setting of the -Nthreads value via their package commands, but there is only a -single global Nthreads value used by OpenMP. Thus if both package -commands are invoked, you should insure the two values are consistent. -If they are not, the last one invoked will take precedence, for both -packages. Also note that if the "-sf hybrid intel omp" command-line"> -switch is used, it invokes a "package -intel" command, followed by a "package omp" command, both with a -setting of Nthreads = 0. -

    -

    The mode keyword determines the precision mode to use for -computing pair style forces, either on the CPU or on the coprocessor, -when using a USER-INTEL supported pair style. It -can take a value of single, mixed which is the default, or -double. Single means single precision is used for the entire -force calculation. Mixed means forces between a pair of atoms are -computed in single precision, but accumulated and stored in double -precision, including storage of forces, torques, energies, and virial -quantities. Double means double precision is used for the entire -force calculation. -

    -

    The balance keyword sets the fraction of pair -style work offloaded to the coprocessor for split -values between 0.0 and 1.0 inclusive. While this fraction of work is -running on the coprocessor, other calculations will run on the host, -including neighbor and pair calculations that are not offloaded, as -well as angle, bond, dihedral, kspace, and some MPI communications. -If split is set to -1, the fraction of work is dynamically adjusted -automatically throughout the run. This typically give performance -within 5 to 10 percent of the optimal fixed fraction. -

    -

    The ghost keyword determines whether or not ghost atoms, i.e. atoms -at the boundaries of proessor sub-domains, are offloaded for neighbor -and force calculations. When the value = "no", ghost atoms are not -offloaded. This option can reduce the amount of data transfer with -the coprocessor and can also overlap MPI communication of forces with -computation on the coprocessor when the newton pair -setting is "on". When the value = "yes", ghost atoms are offloaded. -In some cases this can provide better performance, especially if the -balance fraction is high. -

    -

    The tpc keyword sets the max # of coprocessor threads Ntpc that -will run on each core of the coprocessor. The default value = 4, -which is the number of hardware threads per core supported by the -current generation Xeon Phi chips. -

    -

    The tptask keyword sets the max # of coprocessor threads (Ntptask -assigned to each MPI task. The default value = 240, which is the -total # of threads an entire current generation Xeon Phi chip can run -(240 = 60 cores * 4 threads/core). This means each MPI task assigned -to the Phi will enough threads for the chip to run the max allowed, -even if only 1 MPI task is assigned. If 8 MPI tasks are assigned to -the Phi, each will run with 30 threads. If you wish to limit the -number of threads per MPI task, set tptask to a smaller value. -E.g. for tptask = 16, if 8 MPI tasks are assigned, each will run -with 16 threads, for a total of 128. -

    -

    Note that the default settings for tpc and tptask are fine for -most problems, regardless of how many MPI tasks you assign to a Phi. -

    -

    The no_affinity keyword will turn off automatic setting of core -affinity for MPI tasks and OpenMP threads on the host when using -offload to a coprocessor. Affinity settings are used when possible -to prevent MPI tasks and OpenMP threads from being on separate NUMA -domains and to prevent offload threads from interfering with other -processes/threads used for LAMMPS. -

    -
    - -

    The kokkos style invokes settings associated with the use of the -KOKKOS package. -

    -

    All of the settings are optional keyword/value pairs. Each has a -default value as listed below. -

    -

    The neigh keyword determines how neighbor lists are built. A value -of half uses half-neighbor lists, the same as used by most pair -styles in LAMMPS. A value of half/thread uses a thread-safe variant -of the half-neighbor list. It should be used instead of half when -running with more than 1 threads per MPI task on a CPU. A value of -n2 uses an O(N^2) algorithm to build the neighbor list without -binning, where N = # of atoms on a processor. It is typically slower -than the other methods, which use binning. -

    -

    A value of full uses a full neighbor lists and is the default. This -performs twice as much computation as the half option, however that -is often a win because it is thread-safe and doesn't require atomic -operations in the calculation of pair forces. For that reason, full -is the default setting. However, when running in MPI-only mode with 1 -thread per MPI task, half neighbor lists will typically be faster, -just as it is for non-accelerated pair styles. -

    -

    A value of full/cluster is an experimental neighbor style, where -particles interact with all particles within a small cluster, if at -least one of the clusters particles is within the neighbor cutoff -range. This potentially allows for better vectorization on -architectures such as the Intel Phi. If also reduces the size of the -neighbor list by roughly a factor of the cluster size, thus reducing -the total memory footprint considerably. -

    -

    The newton keyword sets the Newton flags for pairwise and bonded -interactions to off or on, the same as the newton -command allows. The default is off because this will almost always -give better performance for the KOKKOS package. This means more -computation is done, but less communication. However, when running in -MPI-only mode with 1 thread per MPI task, a value of on will -typically be faster, just as it is for non-accelerated pair styles. -

    -

    The binsize keyword sets the size of bins used to bin atoms in -neighbor list builds. The same value can be set by the neigh_modify -binsize command. Making it an option in the -package kokkos command allows it to be set from the command line. The -default value is 0.0, which means the LAMMPS default will be used, -which is bins = 1/2 the size of the pairwise cutoff + neighbor skin -distance. This is fine when neighbor lists are built on the CPU. For -GPU builds, a 2x larger binsize equal to the pairwise cutoff + -neighbor skin, is often faster, which can be set by this keyword. -Note that if you use a longer-than-usual pairwise cutoff, e.g. to -allow for a smaller fraction of KSpace work with a long-range -Coulombic solver because the GPU is faster at -performing pairwise interactions, then this rule of thumb may give too -large a binsize. -

    -

    The comm and comm/exchange and comm/forward keywords determine -whether the host or device performs the packing and unpacking of data -when communicating per-atom data between processors. "Exchange" -communication happens only on timesteps that neighbor lists are -rebuilt. The data is only for atoms that migrate to new processors. -"Forward" communication happens every timestep. The data is for atom -coordinates and any other atom properties that needs to be updated for -ghost atoms owned by each processor. -

    -

    The comm keyword is simply a short-cut to set the same value -for both the comm/exchange and comm/forward keywords. -

    -

    The value options for all 3 keywords are no or host or device. -A value of no means to use the standard non-KOKKOS method of -packing/unpacking data for the communication. A value of host means -to use the host, typically a multi-core CPU, and perform the -packing/unpacking in parallel with threads. A value of device means -to use the device, typically a GPU, to perform the packing/unpacking -operation. -

    -

    The optimal choice for these keywords depends on the input script and -the hardware used. The no value is useful for verifying that the -Kokkos-based host and device values are working correctly. It may -also be the fastest choice when using Kokkos styles in MPI-only mode -(i.e. with a thread count of 1). -

    -

    When running on CPUs or Xeon Phi, the host and device values work -identically. When using GPUs, the device value will typically be -optimal if all of your styles used in your input script are supported -by the KOKKOS package. In this case data can stay on the GPU for many -timesteps without being moved between the host and GPU, if you use the -device value. This requires that your MPI is able to access GPU -memory directly. Currently that is true for OpenMPI 1.8 (or later -versions), Mvapich2 1.9 (or later), and CrayMPI. If your script uses -styles (e.g. fixes) which are not yet supported by the KOKKOS package, -then data has to be move between the host and device anyway, so it is -typically faster to let the host handle communication, by using the -host value. Using host instead of no will enable use of -multiple threads to pack/unpack communicated data. -

    -
    - -

    The omp style invokes settings associated with the use of the -USER-OMP package. -

    -

    The Nthread argument sets the number of OpenMP threads allocated for -each MPI task. For example, if your system has nodes with dual -quad-core processors, it has a total of 8 cores per node. You could -use two MPI tasks per node (e.g. using the -ppn option of the mpirun -command in MPICH or -npernode in OpenMPI), and set Nthreads = 4. -This would use all 8 cores on each node. Note that the product of MPI -tasks * threads/task should not exceed the physical number of cores -(on a node), otherwise performance will suffer. -

    -

    Setting Nthread = 0 instructs LAMMPS to use whatever value is the -default for the given OpenMP environment. This is usually determined -via the OMP_NUM_THREADS environment variable or the compiler -runtime. Note that in most cases the default for OpenMP capable -compilers is to use one thread for each available CPU core when -OMP_NUM_THREADS is not explicitly set, which can lead to poor -performance. -

    -

    Here are examples of how to set the environment variable when -launching LAMMPS: -

    -
    env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
-env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
-mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script 
-
    -

    or you can set it permanently in your shell's start-up script. -All three of these examples use a total of 4 CPU cores. -

    -

    Note that different MPI implementations have different ways of passing -the OMP_NUM_THREADS environment variable to all MPI processes. The -2nd example line above is for MPICH; the 3rd example line with -x is -for OpenMPI. Check your MPI documentation for additional details. -

    -

    What combination of threads and MPI tasks gives the best performance -is difficult to predict and can depend on many components of your -input. Not all features of LAMMPS support OpenMP threading via the -USER-OMP packaage and the parallel efficiency can be very different, -too. -

    -

    Optional keyword/value pairs can also be specified. Each has a -default value as listed below. -

    -

    The neigh keyword specifies whether neighbor list building will be -multi-threaded in addition to force calculations. If neigh is set -to no then neighbor list calculation is performed only by MPI tasks -with no OpenMP threading. If mode is yes (the default), a -multi-threaded neighbor list build is used. Using neigh = yes is -almost always faster and should produce idential neighbor lists at the -expense of using more memory. Specifically, neighbor list pages are -allocated for all threads at the same time and each thread works -within its own pages. -

    -
    - -

    Restrictions: -

    -

    This command cannot be used after the simulation box is defined by a -read_data or create_box command. -

    -

    The cuda style of this command can only be invoked if LAMMPS was built -with the USER-CUDA package. See the Making -LAMMPS section for more info. -

    -

    The gpu style of this command can only be invoked if LAMMPS was built -with the GPU package. See the Making -LAMMPS section for more info. -

    -

    The intel style of this command can only be invoked if LAMMPS was -built with the USER-INTEL package. See the Making -LAMMPS section for more info. -

    -

    The kk style of this command can only be invoked if LAMMPS was built -with the KOKKOS package. See the Making -LAMMPS section for more info. -

    -

    The omp style of this command can only be invoked if LAMMPS was built -with the USER-OMP package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    suffix, "-pk" command-line -setting -

    -

    Default: -

    -

    For the USER-CUDA package, the default is Ngpu = 1 and the option -defaults are newton = off, gpuID = 0 to Ngpu-1, timing = not enabled, -test = not enabled, and thread = auto. These settings are made -automatically by the required "-c on" command-line -switch. You can change them bu using the -package cuda command in your input script or via the "-pk cuda" -command-line switch. -

    -

    For the GPU package, the default is Ngpu = 1 and the option defaults -are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 -to Ngpu-1, tpa = 1, and device = not used. These settings are made -automatically if the "-sf gpu" command-line -switch is used. If it is not used, you -must invoke the package gpu command in your input script or via the -"-pk gpu" command-line switch. -

    -

    For the USER-INTEL package, the default is Nphi = 1 and the option -defaults are omp = 0, mode = mixed, balance = -1, tpc = 4, tptask = -240. The default ghost option is determined by the pair style being -used. This value is output to the screen in the offload report at the -end of each run. Note that all of these settings, except "omp" and -"mode", are ignored if LAMMPS was not built with Xeon Phi coprocessor -support. These settings are made automatically if the "-sf intel" -command-line switch is used. If it is -not used, you must invoke the package intel command in your input -script or or via the "-pk intel" command-line -switch. -

    -

    For the KOKKOS package, the option defaults neigh = full, newton = -off, binsize = 0.0, and comm = host. These settings are made -automatically by the required "-k on" command-line -switch. You can change them bu using the -package kokkos command in your input script or via the "-pk kokkos" -command-line switch. -

    -

    For the OMP package, the default is Nthreads = 0 and the option -defaults are neigh = yes. These settings are made automatically if -the "-sf omp" command-line switch is -used. If it is not used, you must invoke the package omp command in -your input script or via the "-pk omp" command-line -switch. -

    - diff --git a/doc/doc2/pair_adp.html b/doc/doc2/pair_adp.html deleted file mode 100644 index bbce04db07..0000000000 --- a/doc/doc2/pair_adp.html +++ /dev/null @@ -1,194 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style adp command -

    -

    pair_style adp/omp command -

    -

    Syntax: -

    -
    pair_style adp 
-
    -

    Examples: -

    -
    pair_style adp
-pair_coeff * * Ta.adp Ta
-pair_coeff * * ../potentials/AlCu.adp Al Al Cu 
-
    -

    Description: -

    -

    Style adp computes pairwise interactions for metals and metal alloys -using the angular dependent potential (ADP) of (Mishin), -which is a generalization of the embedded atom method (EAM) -potential. The LAMMPS implementation is discussed in -(Singh). The total energy Ei of an atom I is given by -

    -
    -
    -

    where F is the embedding energy which is a function of the atomic -electron density rho, phi is a pair potential interaction, alpha and -beta are the element types of atoms I and J, and s and t = 1,2,3 and -refer to the cartesian coordinates. The mu and lambda terms represent -the dipole and quadruple distortions of the local atomic environment -which extend the original EAM framework by introducing angular forces. -

    -

    Note that unlike for other potentials, cutoffs for ADP potentials are -not set in the pair_style or pair_coeff command; they are specified in -the ADP potential files themselves. Likewise, the ADP potential files -list atomic masses; thus you do not need to use the mass -command to specify them. -

    -

    The NIST WWW site distributes and documents ADP potentials: -

    -
    http://www.ctcms.nist.gov/potentials 
-
    -

    Note that these must be converted into the extended DYNAMO setfl -format discussed below. -

    -

    The NIST site is maintained by Chandler Becker (cbecker at nist.gov) -who is good resource for info on interatomic potentials and file -formats. -

    -
    - -

    Only a single pair_coeff command is used with the adp style which -specifies an extended DYNAMO setfl file, which contains information -for M elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of extended setfl elements to atom types -
    -

    See the pair_coeff doc page for alternate ways to -specify the path for the potential file. -

    -

    As an example, the potentials/AlCu.adp file, included in the -potentials directory of the LAMMPS distrbution, is an extended setfl -file which has tabulated ADP values for w elements and their alloy -interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types -and you want the 1st 3 to be Al, and the 4th to be Cu, you would use -the following pair_coeff command: -

    -
    pair_coeff * * AlCu.adp Al Al Al Cu 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Al arguments map LAMMPS atom types 1,2,3 to the Al -element in the extended setfl file. The final Cu argument maps -LAMMPS atom type 4 to the Al element in the extended setfl file. -Note that there is no requirement that your simulation use all the -elements specified by the extended setfl file. -

    -

    If a mapping value is specified as NULL, the mapping is not performed. -This can be used when an adp potential is used as part of the -hybrid pair style. The NULL values are placeholders for atom types -that will be used with other potentials. -

    -

    Adp files in the potentials directory of the LAMMPS distribution -have an ".adp" suffix. A DYNAMO setfl file extended for ADP is -formatted as follows. Basically it is the standard setfl format -with additional tabulated functions u and w added to the file after -the tabulated pair potentials. See the pair_eam -command for further details on the setfl format. -

    -
    • lines 1,2,3 = comments (ignored) -
    • line 4: Nelements Element1 Element2 ... ElementN -
    • line 5: Nrho, drho, Nr, dr, cutoff -
    -

    Following the 5 header lines are Nelements sections, one for each -element, each with the following format: -

    -
    • line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC) -
    • embedding function F(rho) (Nrho values) -
    • density function rho(r) (Nr values) -
    -

    Following the Nelements sections, Nr values for each pair potential -phi(r) array are listed for all i,j element pairs in the same format -as other arrays. Since these interactions are symmetric (i,j = j,i) -only phi arrays with i >= j are listed, in the following order: i,j = -(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements, -Nelements). The tabulated values for each phi function are listed as -r*phi (in units of eV-Angstroms), since they are for atom pairs, the -same as for other EAM files. -

    -

    After the phi(r) arrays, each of the u(r) arrays are listed in the -same order with the same assumptions of symmetry. Directly following -the u(r), the w(r) arrays are listed. Note that phi(r) is the only -array tabulated with a scaling by r. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, no special mixing rules are needed, since -the ADP potential files specify alloy interactions explicitly. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair_style and pair_coeff commands in -an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). -

    -

    Related commands: -

    -

    pair_coeff, pair_eam -

    -

    Default: none -

    -
    - - - -

    (Mishin) Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 -(2005). -

    - - -

    (Singh) Singh and Warner, Acta Mater, 58, 5797-5805 (2010), -

    - diff --git a/doc/doc2/pair_airebo.html b/doc/doc2/pair_airebo.html deleted file mode 100644 index 898b04d7a2..0000000000 --- a/doc/doc2/pair_airebo.html +++ /dev/null @@ -1,203 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style airebo command -

    -

    pair_style airebo/omp command -

    -

    pair_style rebo command -

    -

    pair_style rebo/omp command -

    -

    Syntax: -

    -
    pair_style style cutoff LJ_flag TORSION_flag 
-
    -
    • style = airebo or rebo -
    • cutoff = LJ cutoff (sigma scale factor) (AIREBO only) -
    • LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional) -
    • TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional) -
    -

    Examples: -

    -
    pair_style airebo 3.0
-pair_style airebo 2.5 1 0
-pair_coeff * * ../potentials/CH.airebo H C 
-
    -
    pair_style rebo
-pair_coeff * * ../potentials/CH.airebo H C 
-
    -

    Description: -

    -

    The airebo pair style computes the Adaptive Intermolecular Reactive -Empirical Bond Order (AIREBO) Potential of (Stuart) for a -system of carbon and/or hydrogen atoms. Note that this is the initial -formulation of AIREBO from 2000, not the later formulation. The -rebo pair style computes the Reactive Empirical Bond Order (REBO) -Potential of (Brenner). Note that this is the so-called -2nd generation REBO from 2002, not the original REBO from 1990. As -discussed below, 2nd generation REBO is closely related to the intial -AIREBO; it is just a subset of the potential energy terms. -

    -

    The AIREBO potential consists of three terms: -

    -
    -
    -

    By default, all three terms are included. For the airebo style, if -the two optional flag arguments to the pair_style command are -included, the LJ and torsional terms can be turned off. Note that -both or neither of the flags must be included. If both of the LJ an -torsional terms are turned off, it becomes the 2nd-generation REBO -potential, with a small caveat on the spline fitting procedure -mentioned below. This can be specified directly as pair_style rebo -with no additional arguments. -

    -

    The detailed formulas for this potential are given in -(Stuart); here we provide only a brief description. -

    -

    The E_REBO term has the same functional form as the hydrocarbon REBO -potential developed in (Brenner). The coefficients for -E_REBO in AIREBO are essentially the same as Brenner's potential, but -a few fitted spline values are slightly different. For most cases the -E_REBO term in AIREBO will produce the same energies, forces and -statistical averages as the original REBO potential from which it was -derived. The E_REBO term in the AIREBO potential gives the model its -reactive capabilities and only describes short-ranged C-C, C-H and H-H -interactions (r < 2 Angstroms). These interactions have strong -coordination-dependence through a bond order parameter, which adjusts -the attraction between the I,J atoms based on the position of other -nearby atoms and thus has 3- and 4-body dependence. -

    -

    The E_LJ term adds longer-ranged interactions (2 < r < cutoff) using a -form similar to the standard Lennard Jones potential. -The E_LJ term in AIREBO contains a series of switching functions so -that the short-ranged LJ repulsion (1/r^12) does not interfere with -the energetics captured by the E_REBO term. The extent of the E_LJ -interactions is determined by the cutoff argument to the pair_style -command which is a scale factor. For each type pair (C-C, C-H, H-H) -the cutoff is obtained by multiplying the scale factor by the sigma -value defined in the potential file for that type pair. In the -standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale -factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff -would be 10.2 Angstroms. -

    -

    The E_TORSION term is an explicit 4-body potential that describes -various dihedral angle preferences in hydrocarbon configurations. -

    -
    - -

    Only a single pair_coeff command is used with the airebo or rebo -style which specifies an AIREBO potential file with parameters for C -and H. Note that the rebo style in LAMMPS uses the same -AIREBO-formatted potential file. These are mapped to LAMMPS atom -types by specifying N additional arguments after the filename in the -pair_coeff command, where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of AIREBO elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, if your LAMMPS simulation has 4 atom types and you want -the 1st 3 to be C, and the 4th to be H, you would use the following -pair_coeff command: -

    -
    pair_coeff * * CH.airebo C C C H 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three C arguments map LAMMPS atom types 1,2,3 to the C -element in the AIREBO file. The final H argument maps LAMMPS atom -type 4 to the H element in the SW file. If a mapping value is -specified as NULL, the mapping is not performed. This can be used -when a airebo potential is used as part of the hybrid pair style. -The NULL values are placeholders for atom types that will be used with -other potentials. -

    -

    The parameters/coefficients for the AIREBO potentials are listed in -the CH.airebo file to agree with the original (Stuart) -paper. Thus the parameters are specific to this potential and the way -it was fit, so modifying the file should be done cautiously. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support the pair_modify -mix, shift, table, and tail options. -

    -

    These pair styles do not write their information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package (which it is by -default). See the Making LAMMPS section -for more info. -

    -

    These pair potentials require the newton setting to be -"on" for pair interactions. -

    -

    The CH.airebo potential file provided with LAMMPS (see the potentials -directory) is parameterized for metal units. You can use -the AIREBO or REBO potential with any LAMMPS units, but you would need -to create your own AIREBO potential file with coefficients listed in -the appropriate units if your simulation doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Stuart) Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486 -(2000). -

    - - -

    (Brenner) Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J -Physics: Condensed Matter, 14, 783-802 (2002). -

    - diff --git a/doc/doc2/pair_awpmd.html b/doc/doc2/pair_awpmd.html deleted file mode 100644 index 7ab6be8670..0000000000 --- a/doc/doc2/pair_awpmd.html +++ /dev/null @@ -1,130 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style awpmd/cut command -

    -

    Syntax: -

    -
    pair_style awpmd/cut Rc keyword value ... 
-
    -
    • Rc = global cutoff, -1 means cutoff of half the shortest box length - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = hartree or dproduct or uhf or free or pbc or fix or harm or ermscale or flex_press - -
        hartree value = none
-  dproduct value = none
-  uhf value = none
-  free value = none
-  pbc value = Plen
-    Plen = periodic width of electron = -1 or positive value (distance units)
-  fix value = Flen
-    Flen = fixed width of electron = -1 or positive value (distance units)
-  harm value = width
-    width = harmonic width constraint
-  ermscale value = factor
-    factor = scaling between electron mass and width variable mass
-  flex_press value = none 
-
      - -
    -

    Examples: -

    -
    pair_style awpmd/cut -1
-pair_style awpmd/cut 40.0 uhf free
-pair_coeff * *
-pair_coeff 2 2 20.0 
-
    -

    Description: -

    -

    This pair style contains an implementation of the Antisymmetrized Wave -Packet Molecular Dynamics (AWPMD) method. Need citation here. Need -basic formulas here. Could be links to other documents. -

    -

    Rc is the cutoff. -

    -

    The pair_style command allows for several optional keywords -to be specified. -

    -

    The hartree, dproduct, and uhf keywords specify the form of the -initial trial wave function for the system. If the hartree keyword -is used, then a Hartree multielectron trial wave function is used. If -the dproduct keyword is used, then a trial function which is a -product of two determinants for each spin type is used. If the uhf -keyword is used, then an unrestricted Hartree-Fock trial wave function -is used. -

    -

    The free, pbc, and fix keywords specify a width constraint on -the electron wavepackets. If the free keyword is specified, then there is no -constraint. If the pbc keyword is used and Plen is specified as --1, then the maximum width is half the shortest box length. If Plen -is a positive value, then the value is the maximum width. If the -fix keyword is used and Flen is specified as -1, then electrons -have a constant width that is read from the data file. If Flen is a -positive value, then the constant width for all electrons is set to -Flen. -

    -

    The harm keyword allow oscillations in the width of the -electron wavepackets. More details are needed. -

    -

    The ermscale keyword specifies a unitless scaling factor -between the electron masses and the width variable mass. More -details needed. -

    -

    If the flex_press keyword is used, then a contribution from the -electrons is added to the total virial and pressure of the system. -

    -

    This potential is designed to be used with atom_style -wavepacket definitions, in order to handle the -description of systems with interacting nuclei and explicit electrons. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • cutoff (distance units) -
    -

    For awpmd/cut, the cutoff coefficient is optional. If it is not -used (as in some of the examples above), the default global value -specified in the pair_style command is used. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    The pair_modify mix, shift, table, and tail options -are not relevant for this pair style. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: -

    -

    These are the defaults for the pair_style keywords: hartree for the -initial wavefunction, free for the wavepacket width. -

    - diff --git a/doc/doc2/pair_beck.html b/doc/doc2/pair_beck.html deleted file mode 100644 index e804eb066b..0000000000 --- a/doc/doc2/pair_beck.html +++ /dev/null @@ -1,117 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style beck command -

    -

    pair_style beck/gpu command -

    -

    pair_style beck/omp command -

    -

    Syntax: -

    -
    pair_style beck Rc 
-
    -
    • Rc = cutoff for interactions (distance units) -
    -

    Examples: -

    -
    pair_style beck 8.0
-pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
-pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0 
-
    -

    Description: -

    -

    Style beck computes interactions based on the potential by -(Beck), originally designed for simulation of Helium. It -includes truncation at a cutoff distance Rc. -

    -
    -
    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands. -

    -
    • A (energy units) -
    • B (energy-distance^6 units) -
    • a (distance units) -
    • alpha (1/distance units) -
    • beta (1/distance^6 units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global cutoff -Rc is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, coeffiecients must be specified. -No default miture rules are used. -

    -

    This pair style does not support the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Beck) Beck, Molecular Physics, 14, 311 (1968). -

    - diff --git a/doc/doc2/pair_body.html b/doc/doc2/pair_body.html deleted file mode 100644 index b83a52bdca..0000000000 --- a/doc/doc2/pair_body.html +++ /dev/null @@ -1,124 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style body command -

    -

    Syntax: -

    -
    pair_style body cutoff 
-
    -

    cutoff = global cutoff for interactions (distance units) -

    -

    Examples: -

    -
    pair_style body 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5 
-
    -

    Description: -

    -

    Style body is for use with body particles and calculates pairwise -body/body interactions as well as interactions between body and -point-particles. See Section_howto 14 -of the manual and the body doc page for more details on -using body particles. -

    -

    This pair style is designed for use with the "nparticle" body style, -which is specified as an argument to the "atom-style body" command. -See the body doc page for more details about the body -styles LAMMPS supports. The "nparticle" style treats a body particle -as a rigid body composed of N sub-particles. -

    -

    The coordinates of a body particle are its center-of-mass (COM). If -the COMs of a pair of body particles are within the cutoff (global or -type-specific, as specified above), then all interactions between -pairs of sub-particles in the two body particles are computed. -E.g. if the first body particle has 3 sub-particles, and the second -has 10, then 30 interactions are computed and summed to yield the -total force and torque on each body particle. -

    -

    IMPORTANT NOTE: In the example just described, all 30 interactions are -computed even if the distance between a particular pair of -sub-particles is greater than the cutoff. Likewise, no interaction -between two body particles is computed if the two COMs are further -apart than the cutoff, even if the distance between some pairs of -their sub-particles is within the cutoff. Thus care should be used in -defining the cutoff distances for body particles, depending on their -shape and size. -

    -

    Similar rules apply for a body particle interacting with a point -particle. The distance between the two particles is calculated using -the COM of the body particle and the position of the point particle. -If the distance is within the cutoff and the body particle has N -sub-particles, then N interactions with the point particle are -computed and summed. If the distance is not within the cutoff, no -interactions between the body and point particle are computed. -

    -

    The interaction between two sub-particles, or a sub-particle and point -particle, or betwee two point particles is computed as a Lennard-Jones -interaction, using the standard formula -

    -
    -
    -

    where Rc is the cutoff. As explained above, an interaction involving -one or two body sub-particles may be computed even for r > Rc. -

    -

    For style body, the following coefficients must be defined for each -pair of atoms types via the pair_coeff command as in -the examples above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global cutoff -is used. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of this pair style can be mixed. The -default mix value is geometric. See the "pair_modify" command for -details. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Defining particles to be bodies so they participate in body/body or -body/particle interactions requires the use of the atom_style -body command. -

    -

    Related commands: -

    -

    pair_coeff, fix_rigid -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_bop.html b/doc/doc2/pair_bop.html deleted file mode 100644 index 0952ed896d..0000000000 --- a/doc/doc2/pair_bop.html +++ /dev/null @@ -1,460 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style bop command -

    -

    Syntax: -

    -
    pair_style bop keyword ... 
-
    -
  • zero or more keywords may be appended - -
  • keyword = save - -
      save = pre-compute and save some values 
-
    - - -

    Examples: -

    -
    pair_style bop 
-pair_coeff * * ../potentials/CdTe_bop Cd Te
-pair_style bop save
-pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
-comm_modify cutoff 14.70 
-
    -

    Description: -

    -

    The bop pair style computes Bond-Order Potentials (BOP) based on -quantum mechanical theory incorporating both sigma and pi bondings. -By analytically deriving the BOP from quantum mechanical theory its -transferability to different phases can approach that of quantum -mechanical methods. This potential is similar to the original BOP -developed by Pettifor (Pettifor_1, -Pettifor_2, Pettifor_3) and later updated -by Murdick, Zhou, and Ward (Murdick, Ward). -Currently, BOP potential files for these systems are provided with -LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with -only a subset of these elements, including a single element (e.g. C or -Cu or Al or Ga or Zn or CdZn), can also be modeled by using the -appropriate alloy file and assigning all atom types to the -singleelement or subset of elements via the pair_coeff command, as -discussed below. -

    -

    The BOP potential consists of three terms: -

    -
    -
    -

    where phi_ij(r_ij) is a short-range two-body function representing the -repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and -beta_(sigma,ij)(r_ij) are respectively sigma and pi bond ingtegrals, -THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and -U_prom is the promotion energy for sp-valent systems. -

    -

    The detailed formulas for this potential are given in Ward -(Ward); here we provide only a brief description. -

    -

    The repulsive energy phi_ij(r_ij) and the bond integrals -beta_(sigma,ij)(r_ij) and beta_(phi,ij)(r_ij) are functions of the -interatomic distance r_ij between atom i and j. Each of these -potentials has a smooth cutoff at a radius of r_(cut,ij). These -smooth cutoffs ensure stable behavior at situations with high sampling -near the cutoff such as melts and surfaces. -

    -

    The bond-orders can be viewed as environment-dependent local variables -that are ij bond specific. The maximum value of the sigma bond-order -(THETA_sigma) is 1, while that of the pi bond-order (THETA_pi) is 2, -attributing to a maximum value of the total bond-order -(THETA_sigma+THETA_pi) of 3. The sigma and pi bond-orders reflect the -ubiquitous single-, double-, and triple- bond behavior of -chemistry. Their analytical expressions can be derived from tight- -binding theory by recursively expanding an inter-site Green's function -as a continued fraction. To accurately represent the bonding with a -computationally efficient potential formulation suitable for MD -simulations, the derived BOP only takes (and retains) the first two -levels of the recursive representations for both the sigma and the pi -bond-orders. Bond-order terms can be understood in terms of molecular -orbital hopping paths based upon the Cyrot-Lackmann theorem -(Pettifor_1). The sigma bond-order with a half-full -valence shell is used to interpolate the bond-order expressiont that -incorporated explicite valance band filling. This pi bond-order -expression also contains also contains a three-member ring term that -allows implementation of an asymmetric density of states, which helps -to either stabilize or destabilize close-packed structures. The pi -bond-order includes hopping paths of length 4. This enables the -incorporation of dihedral angles effects. -

    -

    IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for BOP -potentials are not set in the pair_style or pair_coeff command; they -are specified in the BOP potential files themselves. Likewise, the -BOP potential files list atomic masses; thus you do not need to use -the mass command to specify them. Note that for BOP -potentials with hydrogen, you will likely want to set the mass of H -atoms to be 10x or 20x larger to avoid having to use a tiny timestep. -You can do this by using the mass command after using the -pair_coeff command to read the BOP potential -file. -

    -

    One option can be specified as a keyword with the pair_style command. -

    -

    The save keyword gives you the option to calculate in advance and -store a set of distances, angles, and derivatives of angles. The -default is to not do this, but to calculate them on-the-fly each time -they are needed. The former may be faster, but takes more memory. -The latter requires less memory, but may be slower. It is best to -test this option to optimize the speed of BOP for your particular -system configuration. -

    -
    - -

    Only a single pair_coeff command is used with the bop style which -specifies a BOP potential file, with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of BOP elements to atom types -
    -

    As an example, imagine the CdTe.bop file has BOP values for Cd -and Te. If your LAMMPS simulation has 4 atoms types and you want the -1st 3 to be Cd, and the 4th to be Te, you would use the following -pair_coeff command: -

    -
    pair_coeff * * CdTe Cd Cd Cd Te 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd -element in the BOP file. The final Te argument maps LAMMPS atom type -4 to the Te element in the BOP file. -

    -

    BOP files in the potentials directory of the LAMMPS distribution -have a ".bop" suffix. The potentials are in tabulated form containing -pre-tabulated pair functions for phi_ij(r_ij), beta_(sigma,ij)(r_ij), -and beta_pi,ij)(r_ij). -

    -

    The parameters/coefficients format for the different kinds of BOP -files are given below with variables matching the formulation of Ward -(Ward) and Zhou (Zhou). Each header line containing a -":" is preceded by a blank line. -

    -
    - -

    No angular table file format: -

    -

    The parameters/coefficients format for the BOP potentials input file -containing pre-tabulated functions of g is given below with variables -matching the formulation of Ward (Ward). This format also -assumes the angular functions have the formulation of (Ward). -

    -
    • Line 1: # elements N -
    -

    The first line is followed by N lines containing the atomic -number, mass, and element symbol of each element. -

    -

    Following the definition of the elements several global variables for -the tabulated functions are given. -

    -
    • Line 1: nr, nBOt (nr is the number of divisions the radius is broken -into for function tables and MUST be a factor of 5; nBOt is the number -of divisions for the tabulated values of THETA_(S,ij) - -
    • Line 2: delta_1-delta_7 (if all are not used in the particular - -
    • formulation, set unused values to 0.0) -
    -

    Following this N lines for e_1-e_N containing p_pi. -

    -
    • Line 3: p_pi (for e_1) -
    • Line 4: p_pi (for e_2 and continues to e_N) -
    -

    The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N -

    -
    • Line 1: r_cut (for e_1-e_1 interactions) - -
    • Line 2: c_sigma, a_sigma, c_pi, a_pi - -
    • Line 3: delta_sigma, delta_pi - -
    • Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) -
    -

    The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N -

    -
    • Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for -g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. Ward -contains the full expressions for the constants as functions of -b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) - -
    • Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) -
    -

    The next section contains a block for each interaction type for the -phi_ij(r_ij). Each block has nr entries with 5 entries per line. -

    -
    • Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e_1-e_1 -interaction type) - -
    • Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues -until nr) - -
    • ... - -
    • Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the -e_1-e_1 interaction type) -
    -

    The next section contains a block for each interaction type for the -beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per -line. -

    -
    • Line 1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), beta_sigma(r4), -beta_sigma(r5) (for the e_1-e_1 interaction type) - -
    • Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9), -beta_sigma(r10) (this continues until nr) - -
    • ... - -
    • Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), -beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) -
    -

    The next section contains a block for each interaction type for -beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line. -

    -
    • Line 1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), beta_pi(r5) -(for the e_1-e_1 interaction type) - -
    • Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9), -beta_pi(r10) (this continues until nr) - -
    • ... - -
    • Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), -beta_pi(r5) (for the e_1-e_2 interaction type) -
    -

    The next section contains a block for each interaction type for the -THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has -nBOt entries with 5 entries per line. -

    -
    • Line 1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), -THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) - -
    • Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8), -THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) - -
    • ... - -
    • Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), -THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) -
    -

    The next section contains a block of N lines for e_1-e_N -

    -
    • Line 1: delta^mu (for e_1) -
    • Line 2: delta^mu (for e_2 and repeats to e_N) -
    -

    The last section contains more constants for e_i-e_j interactions with -i=0->N, j=i->N -

    -
    • Line 1: (A_ij)^(mu*nu) (for e1-e1) -
    • Line 2: (A_ij)^(mu*nu) (for e1-e2 and repeats as above) -
    -
    - -

    Angular spline table file format: -

    -

    The parameters/coefficients format for the BOP potentials input file -containing pre-tabulated functions of g is given below with variables -matching the formulation of Ward (Ward). This format also -assumes the angular functions have the formulation of (Zhou). -

    -
    • Line 1: # elements N -
    -

    The first line is followed by N lines containing the atomic -number, mass, and element symbol of each element. -

    -

    Following the definition of the elements several global variables for -the tabulated functions are given. -

    -
    • Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken -into for function tables and MUST be a factor of 5; ntheta is the power of the -power of the spline used to fit the angular function; nBOt is the number -of divisions for the tabulated values of THETA_(S,ij) - -
    • Line 2: delta_1-delta_7 (if all are not used in the particular - -
    • formulation, set unused values to 0.0) -
    -

    Following this N lines for e_1-e_N containing p_pi. -

    -
    • Line 3: p_pi (for e_1) -
    • Line 4: p_pi (for e_2 and continues to e_N) -
    -

    The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N -

    -
    • Line 1: r_cut (for e_1-e_1 interactions) - -
    • Line 2: c_sigma, a_sigma, c_pi, a_pi - -
    • Line 3: delta_sigma, delta_pi - -
    • Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) -
    -

    The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N -

    -
  • Line 1: g0, g1, g2... (These are coefficients for the angular spline -of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The -function can contain up to 10 term thus 10 constants. The first line -can contain up to five constants. If the spline has more than five -terms the second line will contain the remaining constants The -following lines will then contain the constants for the remainaing g0, -g1, g2... (for e_1-e_1-e_2) and the other three body -interactions - -

    The rest of the table has the same structure as the previous section -(see above). -

    -
    - -

    Angular no-spline table file format: -

    -

    The parameters/coefficients format for the BOP potentials input file -containing pre-tabulated functions of g is given below with variables -matching the formulation of Ward (Ward). This format also -assumes the angular functions have the formulation of (Zhou). -

    -
    • Line 1: # elements N -
    -

    The first two lines are followed by N lines containing the atomic -number, mass, and element symbol of each element. -

    -

    Following the definition of the elements several global variables for -the tabulated functions are given. -

    -
    • Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken -into for function tables and MUST be a factor of 5; ntheta is the number of -divisions for the tabulated values of the g angular function; nBOt is the number -of divisions for the tabulated values of THETA_(S,ij) - -
    • Line 2: delta_1-delta_7 (if all are not used in the particular - -
    • formulation, set unused values to 0.0) -
    -

    Following this N lines for e_1-e_N containing p_pi. -

    -
    • Line 3: p_pi (for e_1) -
    • Line 4: p_pi (for e_2 and continues to e_N) -
    -

    The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N -

    -
    • Line 1: r_cut (for e_1-e_1 interactions) - -
    • Line 2: c_sigma, a_sigma, c_pi, a_pi - -
    • Line 3: delta_sigma, delta_pi - -
    • Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) -
    -

    The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N -

    -
    • Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e_1-e_1-e_1 -interaction type) - -
    • Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues -until ntheta) - -
    • ... - -
    • Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the -e_1-e_1-e_2 interaction type) -
    -

    The rest of the table has the same structure as the previous section (see above). -

    -
    - -

    Mixing, shift, table tail correction, restart: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package (which it is by default). -See the Making LAMMPS section for more -info. -

    -

    These pair potentials require the newtion setting to be -"on" for pair interactions. -

    -

    The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal units. -You can use the BOP potential with any LAMMPS units, but you would need -to create your own BOP potential file with coefficients listed in the -appropriate units if your simulation does not use "metal" units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: -

    -

    non-tabulated potential file, a_0 is non-zero. -

    -
    - - - -

    (Pettifor_1) D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 -(1999). -

    - - -

    (Pettifor_2) D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, -4124 (2000). -

    - - -

    (Pettifor_3) D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 -(2002). -

    - - -

    (Murdick) D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R. -Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006). -

    - - -

    (Ward) D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A. -Zimmerman, Phys. Rev. B, 85,115206 (2012). -

    - - -

    (Zhou) X.W. Zhou, D.K. Ward, M. Foster (TBP). -

    - diff --git a/doc/doc2/pair_born.html b/doc/doc2/pair_born.html deleted file mode 100644 index bd2ba588fd..0000000000 --- a/doc/doc2/pair_born.html +++ /dev/null @@ -1,210 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style born command -

    -

    pair_style born/omp command -

    -

    pair_style born/gpu command -

    -

    pair_style born/coul/long command -

    -

    pair_style born/coul/long/cs command -

    -

    pair_style born/coul/long/cuda command -

    -

    pair_style born/coul/long/gpu command -

    -

    pair_style born/coul/long/omp command -

    -

    pair_style born/coul/msm command -

    -

    pair_style born/coul/msm/omp command -

    -

    pair_style born/coul/wolf command -

    -

    pair_style born/coul/wolf/gpu command -

    -

    pair_style born/coul/wolf/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = born or born/coul/long or born/coul/long/cs or born/coul/msm or born/coul/wolf -
    • args = list of arguments for a particular style -
    -
      born args = cutoff
-    cutoff = global cutoff for non-Coulombic interactions (distance units)
-  born/coul/long or born/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  born/coul/msm args = cutoff (cutoff2)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  born/coul/wolf args = alpha cutoff (cutoff2)
-    alpha = damping parameter (inverse distance units)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
    -

    Examples: -

    -
    pair_style born 10.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
-
    -
    pair_style born/coul/long 10.0
-pair_style born/coul/long/cs 10.0
-pair_style born/coul/long 10.0 8.0
-pair_style born/coul/long/cs 10.0 8.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
-
    -
    pair_style born/coul/msm 10.0
-pair_style born/coul/msm 10.0 8.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
-
    -
    pair_style born/coul/wolf 0.25 10.0
-pair_style born/coul/wolf 0.25 10.0 9.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
-
    -

    Description: -

    -

    The born style computes the Born-Mayer-Huggins or Tosi/Fumi -potential described in (Fumi and Tosi), given by -

    -
    -
    -

    where sigma is an interaction-dependent length parameter, rho is an -ionic-pair dependent length parameter, and Rc is the cutoff. -

    -

    The styles with coul/long or coul/msm add a Coulombic term as -described for the lj/cut pair styles. An additional -damping factor is applied to the Coulombic term so it can be used in -conjunction with the kspace_style command and its -ewald or pppm of msm option. The Coulombic cutoff specified for -this style means that pairwise interactions within this distance are -computed directly; interactions outside that distance are computed in -reciprocal space. -

    -

    If one cutoff is specified for the born/coul/long and -born/coul/msm style, it is used for both the A,C,D and Coulombic -terms. If two cutoffs are specified, the first is used as the cutoff -for the A,C,D terms, and the second is the cutoff for the Coulombic -term. -

    -

    The born/coul/wolf style adds a Coulombic term as described for the -Wolf potential in the coul/wolf pair style. -

    -

    Style born/coul/long/cs is identical to born/coul/long except that -a term is added for the core/shell model -to allow charges on core and shell particles to be separated by r = -0.0. -

    -

    Note that these potentials are related to the Buckingham -potential. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • A (energy units) -
    • rho (distance units) -
    • sigma (distance units) -
    • C (energy units * distance units^6) -
    • D (energy units * distance units^8) -
    • cutoff (distance units) -
    -

    The second coefficient, rho, must be greater than zero. -

    -

    The last coefficient is optional. If not specified, the global A,C,D -cutoff specified in the pair_style command is used. -

    -

    For born/coul/long and born/coul/wolf no Coulombic cutoff can be -specified for an individual I,J type pair. All type pairs use the -same global Coulombic cutoff specified in the pair_style command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    These styles support the pair_modify shift option -for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair -interaction. -

    -

    The born/coul/long pair style supports the -pair_modify table option ti tabulate the -short-range portion of the long-range Coulombic interaction. -

    -

    These styles support the pair_modify tail option for adding long-range -tail corrections to energy and pressure. -

    -

    Thess styles writes thei information to binary restart -files, so pair_style and pair_coeff commands do not need to be -specified in an input script that reads a restart file. -

    -

    These styles can only be used via the pair keyword of the run_style -respa command. They do not support the inner, -middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    The born/coul/long style is part of the KSPACE package. It is only -enabled if LAMMPS was built with that package (which it is by -default). See the Making LAMMPS section -for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_style buck -

    -

    Default: none -

    -
    - - - -

    Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964), -Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964). -

    - diff --git a/doc/doc2/pair_brownian.html b/doc/doc2/pair_brownian.html deleted file mode 100644 index be855698da..0000000000 --- a/doc/doc2/pair_brownian.html +++ /dev/null @@ -1,150 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style brownian command -

    -

    pair_style brownian/omp command -

    -

    pair_style brownian/poly command -

    -

    pair_style brownian/poly/omp command -

    -

    Syntax: -

    -
    pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF 
-
    -
    • style = brownian or brownian/poly -
    • mu = dynamic viscosity (dynamic viscosity units) -
    • flaglog = 0/1 log terms in the lubrication approximation on/off -
    • flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects -
    • cutinner = inner cutoff distance (distance units) -
    • cutoff = outer cutoff for interactions (distance units) -
    • t_target = target temp of the system (temperature units) -
    • seed = seed for the random number generator (positive integer) -
    • flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions -
    • flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms -
    -

    Examples: -

    -
    pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
-pair_coeff 1 1 2.05 2.8
-pair_coeff * * 
-
    -

    Description: -

    -

    Styles brownian and brownain/poly compute Brownian forces and -torques on finite-size particles. The former requires monodisperse -spherical particles; the latter allows for polydisperse spherical -particles. -

    -

    These pair styles are designed to be used with either the pair_style -lubricate or pair_style -lubricateU commands to provide thermostatting -when dissipative lubrication forces are acting. Thus the parameters -mu, flaglog, flagfld, cutinner, and cutoff should be -specified consistent with the settings in the lubrication pair styles. -For details, refer to either of the lubrication pair styles. -

    -

    The t_target setting is used to specify the target temperature of -the system. The random number seed is used to generate random -numbers for the thermostatting procedure. -

    -

    The flagHI and flagVF settings are optional. Neither should be -used, or both must be defined. -

    -
    - -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • cutinner (distance units) -
    • cutoff (distance units) -
    -

    The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in this section of -the manual. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See this section of the manual for more -instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is geometric. See -the "pair_modify" command for details. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Only spherical monodisperse particles are allowed for pair_style -brownian. -

    -

    Only spherical particles are allowed for pair_style brownian/poly. -

    -

    Related commands: -

    -

    pair_coeff, pair_style -lubricate, pair_style -lubricateU -

    -

    Default: -

    -

    The default settings for the optional args are flagHI = 1 and flagVF = -1. -

    - diff --git a/doc/doc2/pair_buck.html b/doc/doc2/pair_buck.html deleted file mode 100644 index 046d2f7121..0000000000 --- a/doc/doc2/pair_buck.html +++ /dev/null @@ -1,220 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style buck command -

    -

    pair_style buck/cuda command -

    -

    pair_style buck/gpu command -

    -

    pair_style buck/kk command -

    -

    pair_style buck/omp command -

    -

    pair_style buck/coul/cut command -

    -

    pair_style buck/coul/cut/cuda command -

    -

    pair_style buck/coul/cut/gpu command -

    -

    pair_style buck/coul/cut/kk command -

    -

    pair_style buck/coul/cut/omp command -

    -

    pair_style buck/coul/long command -

    -

    pair_style buck/coul/long/cs command -

    -

    pair_style buck/coul/long/cuda command -

    -

    pair_style buck/coul/long/gpu command -

    -

    pair_style buck/coul/long/kk command -

    -

    pair_style buck/coul/long/omp command -

    -

    pair_style buck/coul/msm command -

    -

    pair_style buck/coul/msm/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = buck or buck/coul/cut or buck/coul/long or buck/coul/long/cs or buck/coul/msm -
    • args = list of arguments for a particular style -
    -
      buck args = cutoff
-    cutoff = global cutoff for Buckingham interactions (distance units)
-  buck/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  buck/coul/long or buck/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  buck/coul/msm args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
    -

    Examples: -

    -
    pair_style buck 2.5
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff * * 100.0 1.5 200.0 3.0 
-
    -
    pair_style buck/coul/cut 10.0
-pair_style buck/coul/cut 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 
-
    -
    pair_style buck/coul/long 10.0
-pair_style buck/coul/long/cs 10.0
-pair_style buck/coul/long 10.0 8.0
-pair_style buck/coul/long/cs 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0 
-
    -
    pair_style buck/coul/msm 10.0
-pair_style buck/coul/msm 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0 
-
    -

    Description: -

    -

    The buck style computes a Buckingham potential (exp/6 instead of -Lennard-Jones 12/6) given by -

    -
    -
    -

    where rho is an ionic-pair dependent length parameter, and Rc is the -cutoff on both terms. -

    -

    The styles with coul/cut or coul/long or coul/msm add a -Coulombic term as described for the lj/cut pair styles. -For buck/coul/long and buc/coul/msm, an additional damping factor -is applied to the Coulombic term so it can be used in conjunction with -the kspace_style command and its ewald or pppm -or msm option. The Coulombic cutoff specified for this style means -that pairwise interactions within this distance are computed directly; -interactions outside that distance are computed in reciprocal space. -

    -

    If one cutoff is specified for the born/coul/cut and -born/coul/long and born/coul/msm styles, it is used for both the -A,C and Coulombic terms. If two cutoffs are specified, the first is -used as the cutoff for the A,C terms, and the second is the cutoff for -the Coulombic term. -

    -

    Style buck/coul/long/cs is identical to buck/coul/long except that -a term is added for the core/shell model -to allow charges on core and shell particles to be separated by r = -0.0. -

    -

    Note that these potentials are related to the Born-Mayer-Huggins -potential. -

    -

    IMPORTANT NOTE: For all these pair styles, the terms with A and C are -always cutoff. The additional Coulombic term can be cutoff or -long-range (no cutoff) depending on whether the style name includes -coul/cut or coul/long or coul/msm. If you wish the C/r^6 term to be -long-range (no cutoff), then see the pair_style -buck/long/coul/long command. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • A (energy units) -
    • rho (distance units) -
    • C (energy-distance^6 units) -
    • cutoff (distance units) -
    • cutoff2 (distance units) -
    -

    The second coefficient, rho, must be greater than zero. -

    -

    The latter 2 coefficients are optional. If not specified, the global -A,C and Coulombic cutoffs are used. If only one cutoff is specified, -it is used as the cutoff for both A,C and Coulombic interactions for -this type pair. If both coefficients are specified, they are used as -the A,C and Coulombic cutoffs for this type pair. You cannot specify -2 cutoffs for style buck, since it has no Coulombic terms. -

    -

    For buck/coul/long only the LJ cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    These styles support the pair_modify shift option -for the energy of the exp() and 1/r^6 portion of the pair interaction. -

    -

    The buck/coul/long pair style supports the -pair_modify table option to tabulate the -short-range portion of the long-range Coulombic interaction. -

    -

    These styles support the pair_modify tail option for adding long-range -tail corrections to energy and pressure for the A,C terms in the -pair interaction. -

    -

    These styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    These styles can only be used via the pair keyword of the run_style -respa command. They do not support the inner, -middle, outer keywords. -

    -

    Restrictions: -

    -

    The buck/coul/long style is part of the KSPACE package. The -buck/coul/long/cs style is part of the CORESHELL package. They are -only enabled if LAMMPS was built with that package (which it is by -default). See the Making LAMMPS section -for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_style born -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_buck_long.html b/doc/doc2/pair_buck_long.html deleted file mode 100644 index 77c8a3884b..0000000000 --- a/doc/doc2/pair_buck_long.html +++ /dev/null @@ -1,182 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style buck/long/coul/long command -

    -

    pair_style buck/long/coul/long/omp command -

    -

    Syntax: -

    -
    pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2) 
-
    -
    • flag_buck = long or cut - -
        long = use Kspace long-range summation for the dispersion term 1/r^6
-  cut = use a cutoff 
-
      -
    • flag_coul = long or off - -
        long = use Kspace long-range summation for the Coulombic term 1/r
-  off = omit the Coulombic term 
-
      -
    • cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) - -
    • cutoff2 = global cutoff for Coulombic (optional) (distance units) -
    -

    Examples: -

    -
    pair_style buck/long/coul/long cut off 2.5
-pair_style buck/long/coul/long cut long 2.5 4.0
-pair_style buck/long/coul/long long long 4.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 3 4 
-
    -

    Description: -

    -

    The buck/long/coul/long style computes a Buckingham potential (exp/6 -instead of Lennard-Jones 12/6) and Coulombic potential, given by -

    -
    -
    -
    -
    -

    Rc is the cutoff. If one cutoff is specified in the pair_style -command, it is used for both the Buckingham and Coulombic terms. If -two cutoffs are specified, they are used as cutoffs for the Buckingham -and Coulombic terms respectively. -

    -

    The purpose of this pair style is to capture long-range interactions -resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r -interactions. This is done by use of the flag_buck and flag_coul -settings. The "Ismail paper has more details on when it is -appropriate to include long-range 1/r^6 interactions, using this -potential. -

    -

    If flag_buck is set to long, no cutoff is used on the Buckingham -1/r^6 dispersion term. The long-range portion can be calculated by -using the kspace_style ewald/disp or pppm/disp -commands. The specified Buckingham cutoff then determines which -portion of the Buckingham interactions are computed directly by the -pair potential versus which part is computed in reciprocal space via -the Kspace style. If flag_buck is set to cut, the Buckingham -interactions are simply cutoff, as with pair_style -buck. -

    -

    If flag_coul is set to long, no cutoff is used on the Coulombic -interactions. The long-range portion can calculated by using any of -several kspace_style command options such as -pppm or ewald. Note that if flag_buck is also set to long, then -the ewald/disp or pppm/disp Kspace style needs to be used to -perform the long-range calculations for both the Buckingham and -Coulombic interactions. If flag_coul is set to off, Coulombic -interactions are not computed. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • A (energy units) -
    • rho (distance units) -
    • C (energy-distance^6 units) -
    • cutoff (distance units) -
    • cutoff2 (distance units) -
    -

    The second coefficient, rho, must be greater than zero. -

    -

    The latter 2 coefficients are optional. If not specified, the global -Buckingham and Coulombic cutoffs specified in the pair_style command -are used. If only one cutoff is specified, it is used as the cutoff -for both Buckingham and Coulombic interactions for this type pair. If -both coefficients are specified, they are used as the Buckingham and -Coulombic cutoffs for this type pair. Note that if you are using -flag_buck set to long, you cannot specify a Buckingham cutoff for -an atom type pair, since only one global Buckingham cutoff is allowed. -Similarly, if you are using flag_coul set to long, you cannot -specify a Coulombic cutoff for an atom type pair, since only one -global Coulombic cutoff is allowed. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair styles does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This pair style supports the pair_modify shift -option for the energy of the exp() and 1/r^6 portion of the pair -interaction, assuming flag_buck is cut. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the Buckingham portion of the pair -interaction. -

    -

    This pair style supports the pair_modify table and -table/disp options since they can tabulate the short-range portion of -the long-range Coulombic and dispersion interactions. -

    -

    This pair style write its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style supports the use of the inner, middle, and outer -keywords of the run_style respa command, meaning the -pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the run_style command for -details. -

    -
    - -

    Restrictions: -

    -

    This style is part of the KSPACE package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. Note that -the KSPACE package is installed by default. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Ismail) Ismail, Tsige, In 't Veld, Grest, Molecular Physics -(accepted) (2007). -

    - diff --git a/doc/doc2/pair_charmm.html b/doc/doc2/pair_charmm.html deleted file mode 100644 index a36e852678..0000000000 --- a/doc/doc2/pair_charmm.html +++ /dev/null @@ -1,219 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/charmm/coul/charmm command -

    -

    pair_style lj/charmm/coul/charmm/cuda command -

    -

    pair_style lj/charmm/coul/charmm/omp command -

    -

    pair_style lj/charmm/coul/charmm/implicit command -

    -

    pair_style lj/charmm/coul/charmm/implicit/cuda command -

    -

    pair_style lj/charmm/coul/charmm/implicit/omp command -

    -

    pair_style lj/charmm/coul/long command -

    -

    pair_style lj/charmm/coul/long/cuda command -

    -

    pair_style lj/charmm/coul/long/gpu command -

    -

    pair_style lj/charmm/coul/long/intel command -

    -

    pair_style lj/charmm/coul/long/opt command -

    -

    pair_style lj/charmm/coul/long/omp command -

    -

    pair_style lj/charmm/coul/msm command -

    -

    pair_style lj/charmm/coul/msm/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = lj/charmm/coul/charmm or lj/charmm/coul/charmm/implicit or lj/charmm/coul/long or lj/charmm/coul/msm -
    • args = list of arguments for a particular style -
    -
      lj/charmm/coul/charmm args = inner outer (inner2) (outer2)
-    inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
-    inner2, outer2 = global switching cutoffs for Coulombic (optional)
-  lj/charmm/coul/charmm/implicit args = inner outer (inner2) (outer2)
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
-    inner2, outer2 = global switching cutoffs for Coulombic (optional)
-  lj/charmm/coul/long args = inner outer (cutoff)
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
-    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
-  lj/charmm/coul/msm args = inner outer (cutoff)
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
-    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) 
-
    -

    Examples: -

    -
    pair_style lj/charmm/coul/charmm 8.0 10.0
-pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5 
-
    -
    pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
-pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5 
-
    -
    pair_style lj/charmm/coul/long 8.0 10.0
-pair_style lj/charmm/coul/long 8.0 10.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5 
-
    -
    pair_style lj/charmm/coul/msm 8.0 10.0
-pair_style lj/charmm/coul/msm 8.0 10.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5 
-
    -

    Description: -

    -

    The lj/charmm styles compute LJ and Coulombic interactions with an -additional switching function S(r) that ramps the energy and force -smoothly to zero between an inner and outer cutoff. It is a widely -used potential in the CHARMM MD code. -See (MacKerell) for a description of the CHARMM force -field. -

    -
    -
    -

    Both the LJ and Coulombic terms require an inner and outer cutoff. -They can be the same for both formulas or different depending on -whether 2 or 4 arguments are used in the pair_style command. In each -case, the inner cutoff distance must be less than the outer cutoff. -It it typical to make the difference between the 2 cutoffs about 1.0 -Angstrom. -

    -

    Style lj/charmm/coul/charmm/implicit computes the same formulas as -style lj/charmm/coul/charmm except that an additional 1/r term is -included in the Coulombic formula. The Coulombic energy thus varies -as 1/r^2. This is effectively a distance-dependent dielectric term -which is a simple model for an implicit solvent with additional -screening. It is designed for use in a simulation of an unsolvated -biomolecule (no explicit water molecules). -

    -

    Styles lj/charmm/coul/long and lj/charmm/coul/msm compute the same -formulas as style lj/charmm/coul/charmm except that an additional -damping factor is applied to the Coulombic term, as described for the -lj/cut pair styles. Only one Coulombic cutoff is -specified for lj/charmm/coul/long and lj/charmm/coul/msm; if only -2 arguments are used in the pair_style command, then the outer LJ -cutoff is used as the single Coulombic cutoff. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • epsilon_14 (energy units) -
    • sigma_14 (distance units) -
    -

    Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. -

    -

    The latter 2 coefficients are optional. If they are specified, they -are used in the LJ formula between 2 atoms of these types which are -also first and fourth atoms in any dihedral. No cutoffs are specified -because this CHARMM force field does not allow varying cutoffs for -individual atom pairs; all pairs use the global cutoff(s) specified in -the pair_style command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14, -and sigma_14 coefficients for all of the lj/charmm pair styles can be -mixed. The default mix value is arithmetic to coincide with the -usual settings for the CHARMM force field. See the "pair_modify" -command for details. -

    -

    None of the lj/charmm pair styles support the -pair_modify shift option, since the Lennard-Jones -portion of the pair interaction is smoothed to 0.0 at the cutoff. -

    -

    The lj/charmm/coul/long style supports the -pair_modify table option since it can tabulate the -short-range portion of the long-range Coulombic interaction. -

    -

    None of the lj/charmm pair styles support the -pair_modify tail option for adding long-range tail -corrections to energy and pressure, since the Lennard-Jones portion of -the pair interaction is smoothed to 0.0 at the cutoff. -

    -

    All of the lj/charmm pair styles write their information to binary -restart files, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. -

    -

    The lj/charmm/coul/long pair style supports the use of the inner, -middle, and outer keywords of the run_style respa -command, meaning the pairwise forces can be partitioned by distance at -different levels of the rRESPA hierarchy. The other styles only -support the pair keyword of run_style respa. See the -run_style command for details. -

    -
    - -

    Restrictions: -

    -

    The lj/charmm/coul/charmm and lj/charmm/coul/charmm/implicit -styles are part of the MOLECULE package. The lj/charmm/coul/long -style is part of the KSPACE package. They are only enabled if LAMMPS -was built with those packages. See the Making -LAMMPS section for more info. Note that -the MOLECULE and KSPACE packages are installed by default. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). -

    - diff --git a/doc/doc2/pair_class2.html b/doc/doc2/pair_class2.html deleted file mode 100644 index 58c66b927c..0000000000 --- a/doc/doc2/pair_class2.html +++ /dev/null @@ -1,193 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/class2 command -

    -

    pair_style lj/class2/cuda command -

    -

    pair_style lj/class2/gpu command -

    -

    pair_style lj/class2/kk command -

    -

    pair_style lj/class2/omp command -

    -

    pair_style lj/class2/coul/cut command -

    -

    pair_style lj/class2/coul/cut/cuda command -

    -

    pair_style lj/class2/coul/cut/kk command -

    -

    pair_style lj/class2/coul/cut/omp command -

    -

    pair_style lj/class2/coul/long command -

    -

    pair_style lj/class2/coul/long/cuda command -

    -

    pair_style lj/class2/coul/long/gpu command -

    -

    pair_style lj/class2/coul/long/kk command -

    -

    pair_style lj/class2/coul/long/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = lj/class2 or lj/class2/coul/cut or lj/class2/coul/long -
    • args = list of arguments for a particular style -
    -
      lj/class2 args = cutoff
-    cutoff = global cutoff for class 2 interactions (distance units)
-  lj/class2/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/class2/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
    -

    Examples: -

    -
    pair_style lj/class2 10.0
-pair_coeff * * 100.0 2.5
-pair_coeff 1 2* 100.0 2.5 9.0 
-
    -
    pair_style lj/class2/coul/cut 10.0
-pair_style lj/class2/coul/cut 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-pair_coeff 1 1 100.0 3.5 9.0 9.0 
-
    -
    pair_style lj/class2/coul/long 10.0
-pair_style lj/class2/coul/long 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0 
-
    -

    Description: -

    -

    The lj/class2 styles compute a 6/9 Lennard-Jones potential given by -

    -
    -
    -

    Rc is the cutoff. -

    -

    The lj/class2/coul/cut and lj/class2/coul/long styles add a -Coulombic term as described for the lj/cut pair styles. -

    -

    See (Sun) for a description of the COMPASS class2 force field. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff1 (distance units) -
    • cutoff2 (distance units) -
    -

    The latter 2 coefficients are optional. If not specified, the global -class 2 and Coulombic cutoffs are used. If only one cutoff is -specified, it is used as the cutoff for both class 2 and Coulombic -interactions for this type pair. If both coefficients are specified, -they are used as the class 2 and Coulombic cutoffs for this type pair. -You cannot specify 2 cutoffs for style lj/class2, since it has no -Coulombic terms. -

    -

    For lj/class2/coul/long only the class 2 cutoff can be specified -since a Coulombic cutoff cannot be specified for an individual I,J -type pair. All type pairs use the same global Coulombic cutoff -specified in the pair_style command. -

    -
    - -

    If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule for epsilon and sigma for -all class2 potentials is to use the sixthpower formulas documented -by the pair_modify command. The pair_modify -mix setting is thus ignored for class2 potentials -for epsilon and sigma. However it is still followed for mixing the -cutoff distance. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/class2 pair styles can be mixed. -Epsilon and sigma are always mixed with the value sixthpower. The -cutoff distance is mixed by whatever option is set by the pair_modify -command (default = geometric). See the "pair_modify" command for -details. -

    -

    All of the lj/class2 pair styles support the -pair_modify shift option for the energy of the -Lennard-Jones portion of the pair interaction. -

    -

    The lj/class2/coul/long pair style does not support the -pair_modify table option since a tabulation -capability has not yet been added to this potential. -

    -

    All of the lj/class2 pair styles support the -pair_modify tail option for adding a long-range -tail correction to the energy and pressure of the Lennard-Jones -portion of the pair interaction. -

    -

    All of the lj/class2 pair styles write their information to binary -restart files, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. -

    -

    All of the lj/class2 pair styles can only be used via the pair -keyword of the run_style respa command. They do not -support the inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    These styles are part of the CLASS2 package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Sun) Sun, J Phys Chem B 102, 7338-7364 (1998). -

    - diff --git a/doc/doc2/pair_coeff.html b/doc/doc2/pair_coeff.html deleted file mode 100644 index fed17fdca0..0000000000 --- a/doc/doc2/pair_coeff.html +++ /dev/null @@ -1,150 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_coeff command -

    -

    Syntax: -

    -
    pair_coeff I J args 
-
    -
    • I,J = atom types (see asterisk form below) -
    • args = coefficients for one or more pairs of atom types -
    -

    Examples: -

    -
    pair_coeff 1 2 1.0 1.0 2.5
-pair_coeff 2 * 1.0 1.0
-pair_coeff 3* 1*2 1.0 1.0 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff * * nialhjea 1 1 2
-pair_coeff * 3 morse.table ENTRY1
-pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid) 
-
    -

    Description: -

    -

    Specify the pairwise force field coefficients for one or more pairs of -atom types. The number and meaning of the coefficients depends on the -pair style. Pair coefficients can also be set in the data file read -by the read_data command or in a restart file. -

    -

    I and J can be specified in one of two ways. Explicit numeric values -can be used for each, as in the 1st example above. I <= J is -required. LAMMPS sets the coefficients for the symmetric J,I -interaction to the same values. -

    -

    A wildcard asterisk can be used in place of or in conjunction with the -I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means all -types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. -

    -

    Note that a pair_coeff command can override a previous setting for the -same I,J pair. For example, these commands set the coeffs for all I,J -pairs, then overwrite the coeffs for just the I,J = 2,3 pair: -

    -
    pair_coeff * * 1.0 1.0 2.5
-pair_coeff 2 3 2.0 1.0 1.12 
-
    -

    A line in a data file that specifies pair coefficients uses the exact -same format as the arguments of the pair_coeff command in an input -script, with the exception of the I,J type arguments. In each line of -the "Pair Coeffs" section of a data file, only a single type I is -specified, which sets the coefficients for type I interacting with -type I. This is because the section has exactly N lines, where N = -the number of atom types. For this reason, the wild-card asterisk -should also not be used as part of the I argument. Thus in a data -file, the line corresponding to the 1st example above would be listed -as -

    -
    2 1.0 1.0 2.5 
-
    -

    For many potentials, if coefficients for type pairs with I != J are -not set explicitly by a pair_coeff command, the values are inferred -from the I,I and J,J settings by mixing rules; see the -pair_modify command for a discussion. Details on -this option as it pertains to individual potentials are described on -the doc page for the potential. -

    -

    Many pair styles, typically for many-body potentials, use tabulated -potential files as input, when specifying the pair_coeff command. -Potential files provided with LAMMPS are in the potentials directory -of the distribution. For some potentials, such as EAM, other archives -of suitable files can be found on the Web. They can be used with -LAMMPS so long as they are in the format LAMMPS expects, as discussed -on the individual doc pages. -

    -

    When a pair_coeff command using a potential file is specified, LAMMPS -looks for the potential file in 2 places. First it looks in the -location specified. E.g. if the file is specified as "niu3.eam", it -is looked for in the current working directory. If it is specified as -"../potentials/niu3.eam", then it is looked for in the potentials -directory, assuming it is a sister directory of the current working -directory. If the file is not found, it is then looked for in the -directory specified by the LAMMPS_POTENTIALS environment variable. -Thus if this is set to the potentials directory in the LAMMPS distro, -then you can use those files from anywhere on your system, without -copying them into your working directory. Environment variables are -set in different ways for different shells. Here are example settings -for -

    -
    csh, tcsh:
-% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials 
-
    -
    bash:
-% export LAMMPS_POTENTIALS=/path/to/lammps/potentials 
-
    -
    Windows:
-% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials 
-
    -
    - -

    The alphabetic list of pair styles defined in LAMMPS is given on the -pair_style doc page. They are also given in more -compact form in the pair section of this -page. -

    -

    Click on the style to display the formula it computes, arguments -specified in the pair_style command, and coefficients specified by the -associated pair_coeff command. -

    -

    Note that there are also additional pair styles (not listed on the -pair_style doc page) submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the pair section of this -page. -

    -

    There are also additional accelerated pair styles (not listed on the -pair_style doc page) included in the LAMMPS -distribution for faster performance on CPUs and GPUs. The list of -these with links to the individual styles are given in the pair -section of this page. -

    -
    - -

    Restrictions: -

    -

    This command must come after the simulation box is defined by a -read_data, read_restart, or -create_box command. -

    -

    Related commands: -

    -

    pair_style, pair_modify, -read_data, read_restart, -pair_write -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_colloid.html b/doc/doc2/pair_colloid.html deleted file mode 100644 index 3f8f006bac..0000000000 --- a/doc/doc2/pair_colloid.html +++ /dev/null @@ -1,213 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style colloid command -

    -

    pair_style colloid/gpu command -

    -

    pair_style colloid/omp command -

    -

    Syntax: -

    -
    pair_style colloid cutoff 
-
    -
    • cutoff = global cutoff for colloidal interactions (distance units) -
    -

    Examples: -

    -
    pair_style colloid 10.0
-pair_coeff * *  25 1.0 10.0 10.0
-pair_coeff 1 1 144 1.0 0.0 0.0 3.0
-pair_coeff 1 2  75.398 1.0 0.0 10.0 9.0
-pair_coeff 2 2  39.478 1.0 10.0 10.0 25.0 
-
    -

    Description: -

    -

    Style colloid computes pairwise interactions between large colloidal -particles and small solvent particles using 3 formulas. A colloidal -particle has a size > sigma; a solvent particle is the usual -Lennard-Jones particle of size sigma. -

    -

    The colloid-colloid interaction energy is given by -

    -
    -
    -

    where A_cc is the Hamaker constant, a1 and a2 are the radii of the two -colloidal particles, and Rc is the cutoff. This equation results from -describing each colloidal particle as an integrated collection of -Lennard-Jones particles of size sigma and is derived in -(Everaers). -

    -

    The colloid-solvent interaction energy is given by -

    -
    -
    -

    where A_cs is the Hamaker constant, a is the radius of the colloidal -particle, and Rc is the cutoff. This formula is derived from the -colloid-colloid interaction, letting one of the particle sizes go to -zero. -

    -

    The solvent-solvent interaction energy is given by the usual -Lennard-Jones formula -

    -
    -
    -

    with A_ss set appropriately, which results from letting both particle -sizes go to zero. -

    -

    When used in combination with pair_style -yukawa/colloid, the two terms become the so-called -DLVO potential, which combines electrostatic repulsion and van der -Waals attraction. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • A (energy units) -
    • sigma (distance units) -
    • d1 (distance units) -
    • d2 (distance units) -
    • cutoff (distance units) -
    -

    A is the Hamaker energy prefactor and should typically be set as -follows: -

    -
    • A_cc = colloid/colloid = 4 pi^2 = 39.5 -
    • A_cs = colloid/solvent = sqrt(A_cc*A_ss) -
    • A_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4) -
    -

    Sigma is the size of the solvent particle or the constituent particles -integrated over in the colloidal particle and should typically be set -as follows: -

    -
    • Sigma_cc = colloid/colloid = 1.0 -
    • Sigma_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma -
    • Sigma_ss = solvent/solvent = 1.0 or whatever size the solvent particle is -
    -

    Thus typically Sigma_cs = 1.0, unless the solvent particle's size != -1.0. -

    -

    D1 and d2 are particle diameters, so that d1 = 2*a1 and d2 = 2*a2 in -the formulas above. Both d1 and d2 must be values >= 0. If d1 > 0 -and d2 > 0, then the pair interacts via the colloid-colloid formula -above. If d1 = 0 and d2 = 0, then the pair interacts via the -solvent-solvent formula. I.e. a d value of 0 is a Lennard-Jones -particle of size sigma. If either d1 = 0 or d2 = 0 and the other is -larger, then the pair interacts via the colloid-solvent formula. -

    -

    Note that the diameter of a particular particle type may appear in -multiple pair_coeff commands, as it interacts with other particle -types. You should insure the particle diameter is specified -consistently each time it appears. -

    -

    The last coefficient is optional. If not specified, the global cutoff -specified in the pair_style command is used. However, you typically -want different cutoffs for interactions between different particle -sizes. E.g. if colloidal particles of diameter 10 are used with -solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5 -would correspond to a colloid-colloid cutoff of 25. A good -rule-of-thumb is to use a colloid-solvent cutoff that is half the big -diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the -colloid-solvent cutoff in this case. -

    -

    IMPORTANT NOTE: When using pair_style colloid for a mixture with 2 (or -more) widely different particles sizes (e.g. sigma=10 colloids in a -background sigam=1 LJ fluid), you will likely want to use these -commands for efficiency: neighbor multi and -comm_modify multi. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the A, sigma, d1, and d2 -coefficients and cutoff distance for this pair style can be mixed. A -is an energy value mixed like a LJ epsilon. D1 and d2 are distance -values and are mixed like sigma. The default mix value is -geometric. See the "pair_modify" command for details. -

    -

    This pair style supports the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Normally, this pair style should be used with finite-size particles -which have a diameter, e.g. see the atom_style -sphere command. However, this is not a requirement, -since the only definition of particle size is via the pair_coeff -parameters for each type. In other words, the physical radius of the -particle is ignored. Thus you should insure that the d1,d2 parameters -you specify are consistent with the physical size of the particles of -that type. -

    -

    Per-particle polydispersity is not yet supported by this pair style; -only per-type polydispersity is enabled via the pair_coeff parameters. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Everaers) Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003). -

    - diff --git a/doc/doc2/pair_comb.html b/doc/doc2/pair_comb.html deleted file mode 100644 index 3812b25920..0000000000 --- a/doc/doc2/pair_comb.html +++ /dev/null @@ -1,204 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style comb command -

    -

    pair_style comb/omp command -

    -

    pair_style comb3 command -

    -

    Syntax: -

    -
    pair_style comb
-pair_style comb3 keyword 
-
    -
    keyword = polar
-  polar value = polar_on or polar_off = whether or not to include atomic polarization 
-
    - - -

    Examples: -

    -
    pair_style comb
-pair_coeff * * ../potentials/ffield.comb Si
-pair_coeff * * ../potentials/ffield.comb Hf Si O 
-
    -
    pair_style comb3 polar_off
-pair_coeff * * ../potentials/ffield.comb3 O Cu N C O 
-
    -

    Description: -

    -

    Style comb computes the second-generation variable charge COMB -(Charge-Optimized Many-Body) potential. Style comb3 computes the -third-generation COMB potential. These COMB potentials are described -in (COMB) and (COMB3). Briefly, the total energy -ET of a system of atoms is given by -

    -
    -
    -

    where Eiself is the self-energy of atom i -(including atomic ionization energies and electron affinities), -Eijshort is the bond-order potential between -atoms i and j, -EijCoul is the Coulomb interactions, -Epolar is the polarization term for organic systems -(style comb3 only), -EvdW is the van der Waals energy (style comb3 only), -Ebarr is a charge barrier function, and -Ecorr are angular correction terms. -

    -

    The COMB potentials (styles comb and comb3) are variable charge -potentials. The equilibrium charge on each atom is calculated by the -electronegativity equalization (QEq) method. See Rick for -further details. This is implemented by the fix -qeq/comb command, which should normally be -specified in the input script when running a model with the COMB -potential. The fix qeq/comb command has options -that determine how often charge equilibration is performed, its -convergence criterion, and which atoms are included in the -calculation. -

    -

    Only a single pair_coeff command is used with the comb and comb3 -styles which specifies the COMB potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the potential file in the pair_coeff -command, where N is the number of LAMMPS atom types. -

    -

    For example, if your LAMMPS simulation of a Si/SiO2/ -HfO2 interface has 4 atom types, and you want the 1st and -last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would -use the following pair_coeff command: -

    -
    pair_coeff * * ../potentials/ffield.comb Si Hf O Si 
-
    -

    The first two arguments must be * * so as to span all LAMMPS atom -types. The first and last Si arguments map LAMMPS atom types 1 and 4 -to the Si element in the ffield.comb file. The second Hf argument -maps LAMMPS atom type 2 to the Hf element, and the third O argument -maps LAMMPS atom type 3 to the O element in the potential file. If a -mapping value is specified as NULL, the mapping is not performed. -This can be used when a comb potential is used as part of the -hybrid pair style. The NULL values are placeholders for atom types -that will be used with other potentials. -

    -

    For style comb, the provided potential file ffield.comb contains -all currently-available 2nd generation COMB parameterizations: for Si, -Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style -comb3, the potential file ffield.comb3 contains all -currently-available 3rd generation COMB paramterizations: O, Cu, N, C, -H, Ti, Zn and Zr. The status of the optimization of the compounds, for -example Cu2O, TiN and hydrocarbons, are given in the -following table: -

    -
    -
    -

    For style comb3, in addition to ffield.comb3, a special parameter -file, lib.comb3, that is exclusively used for C/O/H systems, will be -automatically loaded if carbon atom is detected in LAMMPS input -structure. This file must be in your working directory or in the -directory pointed to by the environment variable LAMMPS_POTENTIALS, as -described on the pair_coeff command doc page. -

    -

    Keyword polar indicates whether the force field includes -the atomic polarization. Since the equilibration of the polarization -has not yet been implemented, it can only set polar_off at present. -

    -

    IMPORTANT NOTE: You can not use potential file ffield.comb with -style comb3, nor file ffield.comb3 with style comb. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. -

    -

    These pair styles does not support the pair_modify -shift, table, and tail options. -

    -

    These pair styles do not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style, pair_coeff, and fix -qeq/comb commands in an input script that reads a -restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    These pair styles are part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

    -

    These pair styles requires the newton setting to be "on" -for pair interactions. -

    -

    The COMB potentials in the ffield.comb and ffield.comb3 files provided -with LAMMPS (see the potentials directory) are parameterized for metal -units. You can use the COMB potential with any LAMMPS -units, but you would need to create your own COMB potential file with -coefficients listed in the appropriate units if your simulation -doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_style, pair_coeff, -fix_qeq/comb -

    -

    Default: none -

    -
    - - - -

    (COMB) T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and -S. R. Phillpot, Phys. Rev. B 81, 125328 (2010) -

    - - -

    (COMB3) T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, -Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, -255-279 (2013). -

    - - -

    (Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 -(1994). -

    - diff --git a/doc/doc2/pair_coul.html b/doc/doc2/pair_coul.html deleted file mode 100644 index db95f8848a..0000000000 --- a/doc/doc2/pair_coul.html +++ /dev/null @@ -1,373 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style coul/cut command -

    -

    pair_style coul/cut/gpu command -

    -

    pair_style coul/cut/kk command -

    -

    pair_style coul/cut/omp command -

    -

    pair_style coul/debye command -

    -

    pair_style coul/debye/gpu command -

    -

    pair_style coul/debye/kk command -

    -

    pair_style coul/debye/omp command -

    -

    pair_style coul/dsf command -

    -

    pair_style coul/dsf/gpu command -

    -

    pair_style coul/dsf/kk command -

    -

    pair_style coul/dsf/omp command -

    -

    pair_style coul/long command -

    -

    pair_style coul/long/cs command -

    -

    pair_style coul/long/omp command -

    -

    pair_style coul/long/gpu command -

    -

    pair_style coul/long/kk command -

    -

    pair_style coul/msm command -

    -

    pair_style coul/msm/omp command -

    -

    pair_style coul/streitz command -

    -

    pair_style coul/wolf command -

    -

    pair_style coul/wolf/kk command -

    -

    pair_style coul/wolf/omp command -

    -

    pair_style tip4p/cut command -

    -

    pair_style tip4p/long command -

    -

    pair_style tip4p/cut/omp command -

    -

    pair_style tip4p/long/omp command -

    -

    Syntax: -

    -
    pair_style coul/cut cutoff
-pair_style coul/debye kappa cutoff
-pair_style coul/dsf alpha cutoff
-pair_style coul/long cutoff
-pair_style coul/long/cs cutoff
-pair_style coul/long/gpu cutoff 
-pair_style coul/wolf alpha cutoff
-pair_style coul/streitz cutoff keyword alpha
-pair_style tip4p/cut otype htype btype atype qdist cutoff
-pair_style tip4p/long otype htype btype atype qdist cutoff 
-
    -
    • cutoff = global cutoff for Coulombic interactions -
    • kappa = Debye length (inverse distance units) -
    • alpha = damping parameter (inverse distance units) -
    -

    Examples: -

    -
    pair_style coul/cut 2.5
-pair_coeff * *
-pair_coeff 2 2 3.5 
-
    -
    pair_style coul/debye 1.4 3.0
-pair_coeff * *
-pair_coeff 2 2 3.5 
-
    -
    pair_style coul/dsf 0.05 10.0
-pair_coeff * * 
-
    -
    pair_style coul/long 10.0
-pair_style coul/long/cs 10.0
-pair_coeff * * 
-
    -
    pair_style coul/msm 10.0
-pair_coeff * * 
-
    -
    pair_style coul/wolf 0.2 9.0
-pair_coeff * * 
-
    -
    pair_style coul/streitz 12.0 ewald
-pair_style coul/streitz 12.0 wolf 0.30
-pair_coeff * * AlO.streitz Al O 
-
    -
    pair_style tip4p/cut 1 2 7 8 0.15 12.0
-pair_coeff * * 
-
    -
    pair_style tip4p/long 1 2 7 8 0.15 10.0
-pair_coeff * * 
-
    -

    Description: -

    -

    The coul/cut style computes the standard Coulombic interaction -potential given by -

    -
    -
    -

    where C is an energy-conversion constant, Qi and Qj are the charges on -the 2 atoms, and epsilon is the dielectric constant which can be set -by the dielectric command. The cutoff Rc truncates -the interaction distance. -

    -
    - -

    Style coul/debye adds an additional exp() damping factor to the -Coulombic term, given by -

    -
    -
    -

    where kappa is the Debye length. This potential is another way to -mimic the screening effect of a polar solvent. -

    -
    - -

    Style coul/dsf computes Coulombic interactions via the damped -shifted force model described in Fennell, given by: -

    -
    -
    -

    where alpha is the damping parameter and erfc() is the -complementary error-function. The potential corrects issues in the -Wolf model (described below) to provide consistent forces and energies -(the Wolf potential is not differentiable at the cutoff) and smooth -decay to zero. -

    -
    - -

    Style coul/wolf computes Coulombic interactions via the Wolf -summation method, described in Wolf, given by: -

    -
    -
    -

    where alpha is the damping parameter, and erc() and erfc() are -error-fuction and complementary error-function terms. This potential -is essentially a short-range, spherically-truncated, -charge-neutralized, shifted, pairwise 1/r summation. With a -manipulation of adding and substracting a self term (for i = j) to the -first and second term on the right-hand-side, respectively, and a -small enough alpha damping parameter, the second term shrinks and -the potential becomes a rapidly-converging real-space summation. With -a long enough cutoff and small enough alpha parameter, the energy and -forces calcluated by the Wolf summation method approach those of the -Ewald sum. So it is a means of getting effective long-range -interactions with a short-range potential. -

    -
    - -

    Style coul/streitz is the Coulomb pair interaction defined as part -of the Streitz-Mintmire potential, as described in this -paper, in which charge distribution about an atom is modeled -as a Slater 1s orbital. More details can be found in the referenced -paper. To fully reproduce the published Streitz-Mintmire potential, -which is a variable charge potential, style coul/streitz must be -used with pair_style eam/alloy (or some other -short-range potential that has been parameterized appropriately) via -the pair_style hybrid/overlay command. Likewise, -charge equilibration must be performed via the fix -qeq/slater command. For example: -

    -
    pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
-pair_coeff * * coul/streitz AlO.streitz Al O
-pair_coeff * * eam/alloy AlO.eam.alloy Al O
-fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz 
-
    -

    The keyword wolf in the coul/streitz command denotes computing -Coulombic interactions via Wolf summation. An additional damping -parameter is required for the Wolf summation, as described for the -coul/wolf potential above. Alternatively, Coulombic interactions can -be computed via an Ewald summation. For example: -

    -
    pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
-kspace_style ewald 1e-6 
-
    -

    Keyword ewald does not need a damping parameter, but a -kspace_style must be defined, which can be style -ewald or pppm. The Ewald method was used in Streitz and -Mintmire's original paper, but a Wolf summation offers a speed-up in -some cases. -

    -

    For the fix qeq/slater command, the qfile can be a filename that -contains QEq parameters as discussed on the fix qeq -command doc page. Alternatively qfile can be replaced by -"coul/streitz", in which case the fix will extract QEq parameters from -the coul/streitz pair style itself. -

    -

    See the examples/strietz directory for an example input script that -uses the Streitz-Mintmire potential. The potentials directory has the -AlO.eam.alloy and AlO.streitz potential files used by the example. -

    -

    Note that the Streiz-Mintmire potential is generally used for oxides, -but there is no conceptual problem with extending it to nitrides and -carbides (such as SiC, TiN). Pair coul/strietz used by itself or with -any other pair style such as EAM, MEAM, Tersoff, or LJ in -hybrid/overlay mode. To do this, you would need to provide a -Streitz-Mintmire parameterizaion for the material being modeled. -

    -
    - -

    Styles coul/long and coul/msm compute the same Coulombic -interactions as style coul/cut except that an additional damping -factor is applied so it can be used in conjunction with the -kspace_style command and its ewald or pppm -option. The Coulombic cutoff specified for this style means that -pairwise interactions within this distance are computed directly; -interactions outside that distance are computed in reciprocal space. -

    -

    Style coul/long/cs is identical to coul/long except that a term is -added for the core/shell model to allow -charges on core and shell particles to be separated by r = 0.0. -

    -

    Styles tip4p/cut and tip4p/long implement the coulomb part of -the TIP4P water model of (Jorgensen), which introduces -a massless site located a short distance away from the oxygen atom -along the bisector of the HOH angle. The atomic types of the oxygen and -hydrogen atoms, the bond and angle types for OH and HOH interactions, -and the distance to the massless charge site are specified as -pair_style arguments. Style tip4p/cut uses a global cutoff for -Coulomb interactions; style tip4p/long is for use with a long-range -Coulombic solver (Ewald or PPPM). -

    -

    IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom -IDs for the O and 2 H atoms must be consecutive, with the O atom -first. This is to enable LAMMPS to "find" the 2 H atoms associated -with each O atom. For example, if the atom ID of an O atom in a TIP4P -water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -

    -

    See the howto section for more -information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighobr list cutoff for Coulomb -interactions is effectively extended by a distance 2*qdist when using -the TIP4P pair style, to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*qdist, to shrink the size of the neighbor list. This leads -to slightly larger cost for the long-range calculation, so you can -test the trade-off for your model. -

    -
    - -

    Note that these potentials are designed to be combined with other pair -potentials via the pair_style hybrid/overlay -command. This is because they have no repulsive core. Hence if they -are used by themselves, there will be no repulsion to keep two -oppositely charged particles from moving arbitrarily close to each -other. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • cutoff (distance units) -
    -

    For coul/cut and coul/debye, the cutoff coefficient is optional. -If it is not used (as in some of the examples above), the default -global value specified in the pair_style command is used. -

    -

    For coul/long and coul/msm no cutoff can be specified for an -individual I,J type pair via the pair_coeff command. All type pairs -use the same global Coulombic cutoff specified in the pair_style -command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the cutoff distance for the -coul/cut style can be mixed. The default mix value is geometric. -See the "pair_modify" command for details. -

    -

    The pair_modify shift option is not relevant -for these pair styles. -

    -

    The coul/long style supports the pair_modify -table option for tabulation of the short-range portion of the -long-range Coulombic interaction. -

    -

    These pair styles do not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    These pair styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    The coul/long, coul/msm and tip4p/long styles are part of the -KSPACE package. The coul/long/cs style is part of the CORESHELL -package. They are only enabled if LAMMPS was built with that package -(which it is by default). See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_style, -hybrid/overlay, kspace_style -

    -

    Default: none -

    -
    - - - -

    (Wolf) D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem -Phys, 110, 8254 (1999). -

    - - -

    (Fennell) C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, -234104 (2006). -

    - - -

    (Streitz) F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003 -(1994). -

    - diff --git a/doc/doc2/pair_coul_diel.html b/doc/doc2/pair_coul_diel.html deleted file mode 100644 index a5f97bce47..0000000000 --- a/doc/doc2/pair_coul_diel.html +++ /dev/null @@ -1,120 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style coul/diel command -

    -

    pair_style coul/diel/omp command -

    -

    Syntax: -

    -
    pair_style coul/diel cutoff 
-
    -

    cutoff = global cutoff (distance units) -

    -

    Examples: -

    -
    pair_style coul/diel 3.5
-pair_coeff 1 4 78. 1.375 0.112 
-
    -

    Description: -

    -

    Style coul/diel computes a Coulomb correction for implict solvent -ion interactions in which the dielectric perimittivity is distance dependent. -The dielectric permittivity epsilon_D(r) connects to limiting regimes: -One limit is defined by a small dielectric permittivity (close to vacuum) -at or close to contact seperation between the ions. At larger separations -the dielectric permittivity reaches a bulk value used in the regular Coulomb -interaction coul/long or coul/cut. -The transition is modeled by a hyperbolic function which is incorporated -in the Coulomb correction term for small ion separations as follows -

    -
    -
    -

    where r_me is the inflection point of epsilon_D(r) and sigma_e is a slope -defining length scale. C is the same Coulomb conversion factor as in the -pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb -interaction between ions is corrected at small distances r. The lower -limit of epsilon_D(r->0)=5.2 due to dielectric saturation (Stiles) -while the Coulomb interaction reaches its bulk limit by setting -epsilon_D(r->\infty)=epsilon, the bulk value of the solvent which is 78 -for water at 298K. -

    -

    Examples of the use of this type of Coulomb interaction include implicit -solvent simulations of salt ions -(Lenart) and of ionic surfactants (Jusufi). -Note that this potential is only reasonable for implicit solvent simulations -and in combiantion with coul/cut or coul/long. It is also usually combined -with gauss/cut, see (Lenart) or (Jusufi). -

    -

    The following coefficients must be defined for each pair of atom -types via the pair_coeff command as in the example -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • epsilon (no units) -
    • r_me (distance units) -
    • sigma_e (distance units) -
    -

    The global cutoff (r_c) specified in the pair_style command is used. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs. -

    -

    This pair style supports the pair_modify shift -option for the energy of the Gauss-potential portion of the pair -interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    This style is part of the "user-misc" package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff -pair_style gauss/cut -

    -

    Default: none -

    -
    - - - -

    (Stiles) Stiles , Hubbard, and Kayser, J Chem Phys, 77, -6189 (1982). -

    - - -

    (Lenart) Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, -044509 (2007). -

    - - -

    (Jusufi) Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, -13783 (2008). -

    - diff --git a/doc/doc2/pair_cs.html b/doc/doc2/pair_cs.html deleted file mode 100644 index 8cc7b4f091..0000000000 --- a/doc/doc2/pair_cs.html +++ /dev/null @@ -1,91 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style born/coul/long/cs command -

    -

    pair_style buck/coul/long/cs command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = born/coul/long/cs or buck/coul/long/cs -
    • args = list of arguments for a particular style -
    -
      born/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  buck/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
    -

    Examples: -

    -
    pair_style born/coul/long/cs 10.0 8.0
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
-
    -
    pair_style buck/coul/long/cs 10.0
-pair_style buck/coul/long/cs 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0 
-
    -

    Description: -

    -

    These pair styles are designed to be used with the adiabatic -core/shell model of (Mitchell and Finchham). See -Section_howto 25 of the manual for an -overview of the model as implemented in LAMMPS. -

    -

    These pair styles are identical to the pair_style -born/coul/long and pair_style -buck/coul/long styles, except they correctly treat the -special case where the distance between two charged core and shell -atoms in the same core/shell pair approach r = 0.0. This needs -special treatment when a long-range solver for Coulombic interactions -is also used, i.e. via the kspace_style command. -

    -

    More specifically, the short-range Coulomb interaction between a core -and its shell should be turned off using the -special_bonds command by setting the 1-2 weight -to 0.0, which works because the core and shell atoms are bonded to -each other. This induces a long-range correction approximation which -fails at small distances (~< 10e-8). Therefore, the Coulomb term which -is used to calculate the correction factor is extended by a minimal -distance (r_min = 1.0-6) when the interaction between a core/shell -pair is treated, as follows -

    -
    -
    -

    where C is an energy-conversion constant, Qi and Qj are the charges on -the core and shell, epsilon is the dielectric constant and r_min is the -minimal distance. -

    -

    Restrictions: -

    -

    These pair styles are part of the CORESHELL package. They are only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_style born, -pair_style buck -

    -

    Default: none -

    -
    - - - -

    (Mitchell and Finchham) Mitchell, Finchham, J Phys Condensed Matter, -5, 1031-1038 (1993). -

    - diff --git a/doc/doc2/pair_dipole.html b/doc/doc2/pair_dipole.html deleted file mode 100644 index 6bce1d0def..0000000000 --- a/doc/doc2/pair_dipole.html +++ /dev/null @@ -1,286 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/cut/dipole/cut command -

    -

    pair_style lj/cut/dipole/cut/gpu command -

    -

    pair_style lj/cut/dipole/cut/omp command -

    -

    pair_style lj/sf/dipole/sf command -

    -

    pair_style lj/sf/dipole/sf/gpu command -

    -

    pair_style lj/sf/dipole/sf/omp command -

    -

    pair_style lj/cut/dipole/long command -

    -

    pair_style lj/long/dipole/long command -

    -

    Syntax: -

    -
    pair_style lj/cut/dipole/cut cutoff (cutoff2)
-pair_style lj/sf/dipole/sf cutoff (cutoff2)
-pair_style lj/cut/dipole/long cutoff (cutoff2)
-pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) 
-
    -
    • cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) - -
    • cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) - -
    • flag_lj = long or cut or off - -
        long = use long-range damping on dispersion 1/r^6 term
-  cut = use a cutoff on dispersion 1/r^6 term
-  off = omit disperion 1/r^6 term entirely 
-
      -
    • flag_coul = long or off - -
        long = use long-range damping on Coulombic 1/r and point-dipole terms
-  off = omit Coulombic and point-dipole terms entirely 
-
      - -
    -

    Examples: -

    -
    pair_style lj/cut/dipole/cut 10.0
-pair_coeff * * 1.0 1.0 
-pair_coeff 2 3 1.0 1.0 2.5 4.0 
-
    -
    pair_style lj/sf/dipole/sf 9.0
-pair_coeff * * 1.0 1.0 
-pair_coeff 2 3 1.0 1.0 2.5 4.0 
-
    -
    pair_style lj/cut/dipole/long 10.0
-pair_coeff * * 1.0 1.0 
-pair_coeff 2 3 1.0 1.0 2.5 4.0 
-
    -
    pair_style lj/long/dipole/long long long 3.5 10.0
-pair_coeff * * 1.0 1.0 
-pair_coeff 2 3 1.0 1.0 2.5 4.0 
-
    -

    Description: -

    -

    Style lj/cut/dipole/cut computes interactions between pairs of particles -that each have a charge and/or a point dipole moment. In addition to -the usual Lennard-Jones interaction between the particles (Elj) the -charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp) -interactions are computed by these formulas for the energy (E), force -(F), and torque (T) between particles I and J. -

    -
    -
    -

    where qi and qj are the charges on the two particles, pi and pj are -the dipole moment vectors of the two particles, r is their separation -distance, and the vector r = Ri - Rj is the separation vector between -the two particles. Note that Eqq and Fqq are simply Coulombic energy -and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the -torques do not act symmetrically. These formulas are discussed in -(Allen) and in (Toukmaji). -

    -

    Style lj/sf/dipole/sf computes "shifted-force" interactions between -pairs of particles that each have a charge and/or a point dipole -moment. In general, a shifted-force potential is a (sligthly) modified -potential containing extra terms that make both the energy and its -derivative go to zero at the cutoff distance; this removes -(cutoff-related) problems in energy conservation and any numerical -instability in the equations of motion (Allen). Shifted-force -interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq), -charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp) -potentials are computed by these formulas for the energy (E), force -(F), and torque (T) between particles I and J: -

    -
    -
    -
    -
    -

    where epsilon and sigma are the standard LJ parameters, r_c is the -cutoff, qi and qj are the charges on the two particles, pi and pj are -the dipole moment vectors of the two particles, r is their separation -distance, and the vector r = Ri - Rj is the separation vector between -the two particles. Note that Eqq and Fqq are simply Coulombic energy -and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the -torques do not act symmetrically. The shifted-force formula for the -Lennard-Jones potential is reported in (Stoddard). The -original (unshifted) formulas for the electrostatic potentials, forces -and torques can be found in (Price). The shifted-force -electrostatic potentials have been obtained by applying equation 5.13 -of (Allen). The formulas for the corresponding forces and -torques have been obtained by applying the 'chain rule' as in appendix -C.3 of (Allen). -

    -

    If one cutoff is specified in the pair_style command, it is used for -both the LJ and Coulombic (q,p) terms. If two cutoffs are specified, -they are used as cutoffs for the LJ and Coulombic (q,p) terms -respectively. -

    -

    Style lj/cut/dipole/long computes long-range point-dipole -interactions as discussed in (Toukmaji). Dipole-dipole, -dipole-charge, and charge-charge interactions are all supported, along -with the standard 12/6 Lennard-Jones interactions, which are computed -with a cutoff. A kspace_style must be defined to -use this pair style. Currently, only kspace_style -ewald/disp support long-range point-dipole -interactions. -

    -

    Style lj/long/dipole/long also computes point-dipole interactions as -discussed in (Toukmaji). Long-range dipole-dipole, -dipole-charge, and charge-charge interactions are all supported, along -with the standard 12/6 Lennard-Jones interactions. LJ interactions -can be cutoff or long-ranged. -

    -

    For style lj/long/dipole/long, if flag_lj is set to long, no -cutoff is used on the LJ 1/r^6 dispersion term. The long-range -portion is calculated by using the kspace_style -ewald_disp command. The specified LJ cutoff then -determines which portion of the LJ interactions are computed directly -by the pair potential versus which part is computed in reciprocal -space via the Kspace style. If flag_lj is set to cut, the LJ -interactions are simply cutoff, as with pair_style -lj/cut. If flag_lj is set to off, LJ interactions -are not computed at all. -

    -

    If flag_coul is set to long, no cutoff is used on the Coulombic or -dipole interactions. The long-range portion is calculated by using -ewald_disp of the kspace_style command. If -flag_coul is set to off, Coulombic and dipole interactions are not -computed at all. -

    -

    Atoms with dipole moments should be integrated using the fix -nve/sphere update dipole command to rotate the -dipole moments. The omega option on the fix -langevin command can be used to thermostat the -rotational motion. The compute temp/sphere -command can be used to monitor the temperature, since it includes -rotational degrees of freedom. The atom_style -dipole command should be used since it defines the -point dipoles and their rotational state. The magnitude of the dipole -moment for each type of particle can be defined by the -dipole command or in the "Dipoles" section of the data -file read in by the read_data command. Their initial -orientation can be defined by the set dipole command or in -the "Atoms" section of the data file. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff1 (distance units) -
    • cutoff2 (distance units) -
    -

    The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distances for this pair style can be mixed. The default -mix value is geometric. See the "pair_modify" command for details. -

    -

    For atom type pairs I,J and I != J, the A, sigma, d1, and d2 -coefficients and cutoff distance for this pair style can be mixed. A -is an energy value mixed like a LJ epsilon. D1 and d2 are distance -values and are mixed like sigma. The default mix value is -geometric. See the "pair_modify" command for details. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the Lennard-Jones portion of the pair -interaction; such energy goes to zero at the cutoff by construction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    The lj/cut/dipole/cut, lj/cut/dipole/long, and -lj/long/dipole/long styles are part of the DIPOLE package. They are -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    The lj/sf/dipole/sf style is part of the USER-MISC package. It is -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Using dipole pair styles with electron units is not -currently supported. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Allen) Allen and Tildesley, Computer Simulation of Liquids, -Clarendon Press, Oxford, 1987. -

    - - -

    (Toukmaji) Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, -10913 (2000). -

    - - -

    (Stoddard) Stoddard and Ford, Phys Rev A, 8, 1504 (1973). -

    - - -

    (Price) Price, Stone and Alderton, Mol Phys, 52, 987 (1984). -

    - diff --git a/doc/doc2/pair_dpd.html b/doc/doc2/pair_dpd.html deleted file mode 100644 index 91d610c71a..0000000000 --- a/doc/doc2/pair_dpd.html +++ /dev/null @@ -1,221 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style dpd command -

    -

    pair_style dpd/gpu command -

    -

    pair_style dpd/omp command -

    -

    pair_style dpd/tstat command -

    -

    pair_style dpd/tstat/gpu command -

    -

    pair_style dpd/tstat/omp command -

    -

    Syntax: -

    -
    pair_style dpd T cutoff seed
-pair_style dpd/tstat Tstart Tstop cutoff seed 
-
    -
    • T = temperature (temperature units) -
    • Tstart,Tstop = desired temperature at start/end of run (temperature units) -
    • cutoff = global cutoff for DPD interactions (distance units) -
    • seed = random # seed (positive integer) -
    -

    Examples: -

    -
    pair_style dpd 1.0 2.5 34387
-pair_coeff * * 3.0 1.0
-pair_coeff 1 1 3.0 1.0 1.0 
-
    -
    pair_style dpd/tstat 1.0 1.0 2.5 34387
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0 1.0 
-
    -

    Description: -

    -

    Style dpd computes a force field for dissipative particle dynamics -(DPD) following the exposition in (Groot). -

    -

    Style dpd/tstat invokes a DPD thermostat on pairwise interactions, -which is equivalent to the non-conservative portion of the DPD force -field. This pair-wise thermostat can be used in conjunction with any -pair style, and in leiu of per-particle thermostats -like fix langevin or ensemble thermostats like -Nose Hoover as implemented by fix nvt. To use -dpd/stat as a thermostat for another pair style, use the pair_style -hybrid/overlay command to compute both the desired -pair interaction and the thermostat for each pair of particles. -

    -

    For style dpd, the force on atom I due to atom J is given as a sum -of 3 terms -

    -
    -
    -

    where Fc is a conservative force, Fd is a dissipative force, and Fr is -a random force. Rij is a unit vector in the direction Ri - Rj, Vij is -the vector difference in velocities of the two atoms = Vi - Vj, alpha -is a Gaussian random number with zero mean and unit variance, dt is -the timestep size, and w(r) is a weighting factor that varies between -0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma), -where Kb is the Boltzmann constant and T is the temperature parameter -in the pair_style command. -

    -

    For style dpd/tstat, the force on atom I due to atom J is the same -as the above equation, except that the conservative Fc term is -dropped. Also, during the run, T is set each timestep to a ramped -value from Tstart to Tstop. -

    -

    For style dpd, the pairwise energy associated with style dpd is -only due to the conservative force term Fc, and is shifted to be zero -at the cutoff distance Rc. The pairwise virial is calculated using -all 3 terms. For style dpd/tstat there is no pairwise energy, but -the last two terms of the formula make a contribution to the virial. -

    -

    For style dpd, the following coefficients must be defined for each -pair of atoms types via the pair_coeff command as in -the examples above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • A (force units) -
    • gamma (force/velocity units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global DPD -cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), -where T is the temperature set by the pair_style -command so it does not need to be specified. -

    -

    For style dpd/tstat, the coefficiencts defined for each pair of -atoms types via the pair_coeff command is the same, -except that A is not included. -

    -

    The GPU-accelerated versions of these styles are implemented based on -the work of (Afshar) and (Phillips). -

    -

    IMPORTANT NOTE: If you are modeling DPD polymer chains, you may want -to use the pair_style srp command in conjuction with -these pair styles. It is a soft segmental repulsive potential (SRP) -that can prevent DPD polymer chains from crossing each other. -

    -

    IMPORTANT NOTE: The virial calculation for pressure when using this -pair style includes all the components of force listed above, -including the random force. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    These pair styles do not support the pair_modify -shift option for the energy of the pair interaction. Note that as -discussed above, the energy due to the conservative Fc term is already -shifted to be 0.0 at the cutoff distance Rc. -

    -

    The pair_modify table option is not relevant -for these pair styles. -

    -

    These pair style do not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    These pair styles writes their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. Note -that the user-specified random number seed is stored in the restart -file, so when a simulation is restarted, each processor will -re-initialize its random number generator the same way it did -initially. This means the random forces will be random, but will not -be the same as they would have been if the original simulation had -continued past the restart time. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -

    The dpd/tstat style can ramp its target temperature over multiple -runs, using the start and stop keywords of the run -command. See the run command for details of how to do -this. -

    -
    - -

    Restrictions: -

    -

    The default frequency for rebuilding neighbor lists is every 10 steps -(see the neigh_modify command). This may be too -infrequent for style dpd simulations since particles move rapidly -and can overlap by large amounts. If this setting yields a non-zero -number of "dangerous" reneighborings (printed at the end of a -simulation), you should experiment with forcing reneighboring more -often and see if system energies/trajectories change. -

    -

    These pair styles requires you to use the comm_modify vel -yes command so that velocites are stored by ghost -atoms. -

    -

    These pair styles will not restart exactly when using the -read_restart command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -read_restart command for more details. -

    -

    Related commands: -

    -

    pair_coeff, fix nvt, fix -langevin, pair_style srp -

    -

    Default: none -

    -
    - - - -

    (Groot) Groot and Warren, J Chem Phys, 107, 4423-35 (1997). -

    - - -

    (Afshar) Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys -Comm, 184, 1119-1128 (2013). -

    - - -

    (Phillips) C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput -Phys Comm, 230, 7191-7201 (2011). -

    - diff --git a/doc/doc2/pair_dsmc.html b/doc/doc2/pair_dsmc.html deleted file mode 100644 index f21cefe8c7..0000000000 --- a/doc/doc2/pair_dsmc.html +++ /dev/null @@ -1,154 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style dsmc command -

    -

    Syntax: -

    -
    pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample 
-
    -
    • max_cell_size = global maximum cell size for DSMC interactions (distance units) -
    • seed = random # seed (positive integer) -
    • weighting = macroparticle weighting -
    • Tref = reference temperature (temperature units) -
    • Nrecompute = recompute v*sigma_max every this many timesteps (timesteps) -
    • Nsample = sample this many times in recomputing v*sigma_max -
    -

    Examples: -

    -
    pair_style dsmc 2.5 34387 10 1.0 100 20
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0 
-
    -

    Description: -

    -

    Style dsmc computes collisions between pairs of particles for a -direct simulation Monte Carlo (DSMC) model following the exposition in -(Bird). Each collision resets the velocities of the two -particles involved. The number of pairwise collisions for each pair -or particle types and the length scale within which they occur are -determined by the parameters of the pair_style and pair_coeff -commands. -

    -

    Stochastic collisions are performed using the variable hard sphere -(VHS) approach, with the user-defined max_cell_size value used as -the maximum DSMC cell size, and reference cross-sections for -collisions given using the pair_coeff command. -

    -

    There is no pairwise energy or virial contributions associated with -this pair style. -

    -

    The following coefficient must be defined for each pair of atoms types -via the pair_coeff command as in the examples above, -or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • sigma (area units, i.e. distance-squared) -
    -

    The global DSMC max_cell_size determines the maximum cell length -used in the DSMC calculation. A structured mesh is overlayed on the -simulation box such that an integer number of cells are created in -each direction for each processor's sub-domain. Cell lengths are -adjusted up to the user-specified maximum cell size. -

    -
    - -

    To perform a DSMC simulation with LAMMPS, several additional options -should be set in your input script, though LAMMPS does not check for -these settings. -

    -

    Since this pair style does not compute particle forces, you should use -the "fix nve/noforce" time integration fix for the DSMC particles, -e.g. -

    -
    fix 1 all nve/noforce 
-
    -

    This pair style assumes that all particles will communicated to -neighboring processors every timestep as they move. This makes it -possible to perform all collisions between pairs of particles that are -on the same processor. To ensure this occurs, you should use -these commands: -

    -
    neighbor 0.0 bin
-neigh_modify every 1 delay 0 check no
-atom_modify sort 0 0.0
-communicate single cutoff 0.0 
-
    -

    These commands ensure that LAMMPS communicates particles to -neighboring processors every timestep and that no ghost atoms are -created. The output statistics for a simulation run should indicate -there are no ghost particles or neighbors. -

    -

    In order to get correct DSMC collision statistics, users should -specify a Gaussian velocity distribution when populating the -simulation domain. Note that the default velocity distribution is -uniform, which will not give good DSMC collision rates. Specify -"dist gaussian" when using the velocity command -as in the following: -

    -
    velocity all create 594.6 87287 loop geom dist gaussian 
-
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. Note -that the user-specified random number seed is stored in the restart -file, so when a simulation is restarted, each processor will -re-initialize its random number generator the same way it did -initially. This means the random forces will be random, but will not -be the same as they would have been if the original simulation had -continued past the restart time. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the MC package. It is only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, fix nve/noforce, -neigh_modify, neighbor, -comm_modify -

    -

    Default: none -

    -
    - - - -

    (Bird) G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation -of Gas Flows" (1994). -

    - diff --git a/doc/doc2/pair_eam.html b/doc/doc2/pair_eam.html deleted file mode 100644 index 3bb2cb901f..0000000000 --- a/doc/doc2/pair_eam.html +++ /dev/null @@ -1,480 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style eam command -

    -

    pair_style eam/cuda command -

    -

    pair_style eam/gpu command -

    -

    pair_style eam/kk command -

    -

    pair_style eam/omp command -

    -

    pair_style eam/opt command -

    -

    pair_style eam/alloy command -

    -

    pair_style eam/alloy/cuda command -

    -

    pair_style eam/alloy/gpu command -

    -

    pair_style eam/alloy/kk command -

    -

    pair_style eam/alloy/omp command -

    -

    pair_style eam/alloy/opt command -

    -

    pair_style eam/cd command -

    -

    pair_style eam/cd/omp command -

    -

    pair_style eam/fs command -

    -

    pair_style eam/fs/cuda command -

    -

    pair_style eam/fs/gpu command -

    -

    pair_style eam/fs/kk command -

    -

    pair_style eam/fs/omp command -

    -

    pair_style eam/fs/opt command -

    -

    Syntax: -

    -
    pair_style style 
-
    -
    • style = eam or eam/alloy or eam/cd or eam/fs -
    -

    Examples: -

    -
    pair_style eam
-pair_coeff * * cuu3
-pair_coeff 1*3 1*3 niu3.eam 
-
    -
    pair_style eam/alloy
-pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni 
-
    -
    pair_style eam/cd
-pair_coeff * * ../potentials/FeCr.cdeam Fe Cr 
-
    -
    pair_style eam/fs
-pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni 
-
    -

    Description: -

    -

    Style eam computes pairwise interactions for metals and metal alloys -using embedded-atom method (EAM) potentials (Daw). The total -energy Ei of an atom I is given by -

    -
    -
    -

    where F is the embedding energy which is a function of the atomic -electron density rho, phi is a pair potential interaction, and alpha -and beta are the element types of atoms I and J. The multi-body -nature of the EAM potential is a result of the embedding energy term. -Both summations in the formula are over all neighbors J of atom I -within the cutoff distance. -

    -

    The cutoff distance and the tabulated values of the functionals F, -rho, and phi are listed in one or more files which are specified by -the pair_coeff command. These are ASCII text files -in a DYNAMO-style format which is described below. DYNAMO was the -original serial EAM MD code, written by the EAM originators. Several -DYNAMO potential files for different metals are included in the -"potentials" directory of the LAMMPS distribution. All of these files -are parameterized in terms of LAMMPS metal units. -

    -

    IMPORTANT NOTE: The eam style reads single-element EAM potentials in -the DYNAMO funcfl format. Either single element or alloy systems -can be modeled using multiple funcfl files and style eam. For the -alloy case LAMMPS mixes the single-element potentials to produce alloy -potentials, the same way that DYNAMO does. Alternatively, a single -DYNAMO setfl file or Finnis/Sinclair EAM file can be used by LAMMPS -to model alloy systems by invoking the eam/alloy or eam/cd or -eam/fs styles as described below. These files require no mixing -since they specify alloy interactions explicitly. -

    -

    IMPORTANT NOTE: Note that unlike for other potentials, cutoffs for EAM -potentials are not set in the pair_style or pair_coeff command; they -are specified in the EAM potential files themselves. Likewise, the -EAM potential files list atomic masses; thus you do not need to use -the mass command to specify them. -

    -

    There are several WWW sites that distribute and document EAM -potentials stored in DYNAMO or other formats: -

    -
    http://www.ctcms.nist.gov/potentials
-http://cst-www.nrl.navy.mil/ccm6/ap
-http://enpub.fulton.asu.edu/cms/potentials/main/main.htm 
-
    -

    These potentials should be usable with LAMMPS, though the alternate -formats would need to be converted to the DYNAMO format used by LAMMPS -and described on this page. The NIST site is maintained by Chandler -Becker (cbecker at nist.gov) who is good resource for info on -interatomic potentials and file formats. -

    -
    - -

    For style eam, potential values are read from a file that is in the -DYNAMO single-element funcfl format. If the DYNAMO file was created -by a Fortran program, it cannot have "D" values in it for exponents. -C only recognizes "e" or "E" for scientific notation. -

    -

    Note that unlike for other potentials, cutoffs for EAM potentials are -not set in the pair_style or pair_coeff command; they are specified in -the EAM potential files themselves. -

    -

    For style eam a potential file must be assigned to each I,I pair of -atom types by using one or more pair_coeff commands, each with a -single argument: -

    -
    • filename -
    -

    Thus the following command -

    -
    pair_coeff *2 1*2 cuu3.eam 
-
    -

    will read the cuu3 potential file and use the tabulated Cu values for -F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs -1,2 and 2,1 are ignored). See the pair_coeff doc -page for alternate ways to specify the path for the potential file. -In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms. -Different single-element files can be assigned to different atom types -to model an alloy system. The mixing to create alloy potentials for -type pairs with I != J is done automatically the same way that the -serial DYNAMO code originally did it; you do not need to specify -coefficients for these type pairs. -

    -

    Funcfl files in the potentials directory of the LAMMPS -distribution have an ".eam" suffix. A DYNAMO single-element funcfl -file is formatted as follows: -

    -
    • line 1: comment (ignored) -
    • line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC) -
    • line 3: Nrho, drho, Nr, dr, cutoff -
    -

    On line 2, all values but the mass are ignored by LAMMPS. The mass is -in mass units, e.g. mass number or grams/mole for metal -units. The cubic lattice constant is in Angstroms. On line 3, Nrho -and Nr are the number of tabulated values in the subsequent arrays, -drho and dr are the spacing in density and distance space for the -values in those arrays, and the specified cutoff becomes the pairwise -cutoff used by LAMMPS for the potential. The units of dr are -Angstroms; I'm not sure of the units for drho - some measure of -electron density. -

    -

    Following the three header lines are three arrays of tabulated values: -

    -
    • embedding function F(rho) (Nrho values) -
    • effective charge function Z(r) (Nr values) -
    • density function rho(r) (Nr values) -
    -

    The values for each array can be listed as multiple values per line, -so long as each array starts on a new line. For example, the -individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr. -

    -

    The units for the embedding function F are eV. The units for the -density function rho are the same as for drho (see above, electron -density). The units for the effective charge Z are "atomic charge" or -sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used -by LAMMPS to compute the pair potential term in the EAM energy -expression as r*phi, in units of eV-Angstroms, via the formula -

    -
    r*phi = 27.2 * 0.529 * Zi * Zj 
-
    -

    where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. -

    -
    - -

    Style eam/alloy computes pairwise interactions using the same -formula as style eam. However the associated -pair_coeff command reads a DYNAMO setfl file -instead of a funcfl file. Setfl files can be used to model a -single-element or alloy system. In the alloy case, as explained -above, setfl files contain explicit tabulated values for alloy -interactions. Thus they allow more generality than funcfl files for -modeling alloys. -

    -

    For style eam/alloy, potential values are read from a file that is -in the DYNAMO multi-element setfl format, except that element names -(Ni, Cu, etc) are added to one of the lines in the file. If the -DYNAMO file was created by a Fortran program, it cannot have "D" -values in it for exponents. C only recognizes "e" or "E" for -scientific notation. -

    -

    Only a single pair_coeff command is used with the eam/alloy style -which specifies a DYNAMO setfl file, which contains information for -M elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of setfl elements to atom types -
    -

    As an example, the potentials/NiAlH_jea.eam.alloy file is a setfl -file which has tabulated EAM values for 3 elements and their alloy -interactions: Ni, Al, and H. See the pair_coeff doc -page for alternate ways to specify the path for the potential file. -If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to -be Ni, and the 4th to be Al, you would use the following pair_coeff -command: -

    -
    pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni -element in the setfl file. The final Al argument maps LAMMPS atom -type 4 to the Al element in the setfl file. Note that there is no -requirement that your simulation use all the elements specified by the -setfl file. -

    -

    If a mapping value is specified as NULL, the mapping is not performed. -This can be used when an eam/alloy potential is used as part of the -hybrid pair style. The NULL values are placeholders for atom types -that will be used with other potentials. -

    -

    Setfl files in the potentials directory of the LAMMPS distribution -have an ".eam.alloy" suffix. A DYNAMO multi-element setfl file is -formatted as follows: -

    -
    • lines 1,2,3 = comments (ignored) -
    • line 4: Nelements Element1 Element2 ... ElementN -
    • line 5: Nrho, drho, Nr, dr, cutoff -
    -

    In a DYNAMO setfl file, line 4 only lists Nelements = the # of -elements in the setfl file. For LAMMPS, the element name (Ni, Cu, -etc) of each element must be added to the line, in the order the -elements appear in the file. -

    -

    The meaning and units of the values in line 5 is the same as for the -funcfl file described above. Note that the cutoff (in Angstroms) is -a global value, valid for all pairwise interactions for all element -pairings. -

    -

    Following the 5 header lines are Nelements sections, one for each -element, each with the following format: -

    -
    • line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC) -
    • embedding function F(rho) (Nrho values) -
    • density function rho(r) (Nr values) -
    -

    As with the funcfl files, only the mass (in mass units, -e.g. mass number or grams/mole for metal units) is used by LAMMPS from -the 1st line. The cubic lattice constant is in Angstroms. The F and -rho arrays are unique to a single element and have the same format and -units as in a funcfl file. -

    -

    Following the Nelements sections, Nr values for each pair potential -phi(r) array are listed for all i,j element pairs in the same format -as other arrays. Since these interactions are symmetric (i,j = j,i) -only phi arrays with i >= j are listed, in the following order: i,j = -(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements, -Nelements). Unlike the effective charge array Z(r) in funcfl files, -the tabulated values for each phi function are listed in setfl files -directly as r*phi (in units of eV-Angstroms), since they are for atom -pairs. -

    -
    - -

    Style eam/cd is similar to the eam/alloy style, except that it -computes alloy pairwise interactions using the concentration-dependent -embedded-atom method (CD-EAM). This model can reproduce the enthalpy -of mixing of alloys over the full composition range, as described in -(Stukowski). -

    -

    The pair_coeff command is specified the same as for the eam/alloy -style. However the DYNAMO setfl file must has two -lines added to it, at the end of the file: -

    -
    • line 1: Comment line (ignored) -
    • line 2: N Coefficient0 Coefficient1 ... CoeffincientN -
    -

    The last line begins with the degree N of the polynomial function -h(x) that modifies the cross interaction between A and B elements. -Then N+1 coefficients for the terms of the polynomial are then -listed. -

    -

    Modified EAM setfl files used with the eam/cd style must contain -exactly two elements, i.e. in the current implementation the eam/cd -style only supports binary alloys. The first and second elements in -the input EAM file are always taken as the A and B species. -

    -

    CD-EAM files in the potentials directory of the LAMMPS -distribution have a ".cdeam" suffix. -

    -
    - -

    Style eam/fs computes pairwise interactions for metals and metal -alloys using a generalized form of EAM potentials due to Finnis and -Sinclair (Finnis). The total energy Ei of an atom I is -given by -

    -
    -
    -

    This has the same form as the EAM formula above, except that rho is -now a functional specific to the atomic types of both atoms I and J, -so that different elements can contribute differently to the total -electron density at an atomic site depending on the identity of the -element at that atomic site. -

    -

    The associated pair_coeff command for style eam/fs -reads a DYNAMO setfl file that has been extended to include -additional rho_alpha_beta arrays of tabulated values. A discussion of -how FS EAM differs from conventional EAM alloy potentials is given in -(Ackland1). An example of such a potential is the same -author's Fe-P FS potential (Ackland2). Note that while FS -potentials always specify the embedding energy with a square root -dependence on the total density, the implementation in LAMMPS does not -require that; the user can tabulate any functional form desired in the -FS potential files. -

    -

    For style eam/fs, the form of the pair_coeff command is exactly the -same as for style eam/alloy, e.g. -

    -
    pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al 
-
    -

    where there are N additional arguments after the filename, where N is -the number of LAMMPS atom types. See the pair_coeff -doc page for alternate ways to specify the path for the potential -file. The N values determine the mapping of LAMMPS atom types to EAM -elements in the file, as described above for style eam/alloy. As -with eam/alloy, if a mapping value is NULL, the mapping is not -performed. This can be used when an eam/fs potential is used as -part of the hybrid pair style. The NULL values are used as -placeholders for atom types that will be used with other potentials. -

    -

    FS EAM files include more information than the DYNAMO setfl format -files read by eam/alloy, in that i,j density functionals for all -pairs of elements are included as needed by the Finnis/Sinclair -formulation of the EAM. -

    -

    FS EAM files in the potentials directory of the LAMMPS distribution -have an ".eam.fs" suffix. They are formatted as follows: -

    -
    • lines 1,2,3 = comments (ignored) -
    • line 4: Nelements Element1 Element2 ... ElementN -
    • line 5: Nrho, drho, Nr, dr, cutoff -
    -

    The 5-line header section is identical to an EAM setfl file. -

    -

    Following the header are Nelements sections, one for each element I, -each with the following format: -

    -
    • line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC) -
    • embedding function F(rho) (Nrho values) -
    • density function rho(r) for element I at element 1 (Nr values) -
    • density function rho(r) for element I at element 2 -
    • ... -
    • density function rho(r) for element I at element Nelement -
    -

    The units of these quantities in line 1 are the same as for setfl -files. Note that the rho(r) arrays in Finnis/Sinclair can be -asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the -file. -

    -

    Following the Nelements sections, Nr values for each pair potential -phi(r) array are listed in the same manner (r*phi, units of -eV-Angstroms) as in EAM setfl files. Note that in Finnis/Sinclair, -the phi(r) arrays are still symmetric, so only phi arrays for i >= j -are listed. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accerlate of the manual for more -instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above with the individual styles. You never need to specify -a pair_coeff command with I != J arguments for the eam styles. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    The eam pair styles do not write their information to binary restart -files, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair_style and pair_coeff commands in -an input script that reads a restart file. -

    -

    The eam pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    All of these styles except the eam/cd style are part of the MANYBODY -package. They are only enabled if LAMMPS was built with that package -(which it is by default). See the Making -LAMMPS section for more info. -

    -

    The eam/cd style is part of the USER-MISC package and also requires -the MANYBODY package. It is only enabled if LAMMPS was built with -those packages. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Ackland1) Ackland, Condensed Matter (2005). -

    - - -

    (Ackland2) Ackland, Mendelev, Srolovitz, Han and Barashev, Journal -of Physics: Condensed Matter, 16, S2629 (2004). -

    - - -

    (Daw) Daw, Baskes, Phys Rev Lett, 50, 1285 (1983). -Daw, Baskes, Phys Rev B, 29, 6443 (1984). -

    - - -

    (Finnis) Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984). -

    - - -

    (Stukowski) Stukowski, Sadigh, Erhart, Caro; Modeling Simulation -Materials Science & Engineering, 7, 075005 (2009). -

    - diff --git a/doc/doc2/pair_edip.html b/doc/doc2/pair_edip.html deleted file mode 100644 index fcf1b3ec4e..0000000000 --- a/doc/doc2/pair_edip.html +++ /dev/null @@ -1,174 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style edip command -

    -

    Syntax: -

    -
    pair_style edip 
-
    -
    pair_style edip/omp 
-
    -

    Examples: -

    -

    pair_style edip -pair_coeff * * Si.edip Si -

    -

    Description: -

    -

    The edip style computes a 3-body EDIP potential which is -popular for modeling silicon materials where it can have advantages -over other models such as the Stillinger-Weber or -Tersoff potentials. In EDIP, the energy E of a -system of atoms is -

    -
    -
    -

    where phi2 is a two-body term and phi3 is a three-body term. The -summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = a. -Both terms depend on the local environment of atom I through its -effective coordination number defined by Z, which is unity for a -cutoff distance < c and gently goes to 0 at distance = a. -

    -

    Only a single pair_coeff command is used with the edip style which -specifies a EDIP potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of EDIP elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine a file Si.edip has EDIP values for Si. -

    -

    EDIP files in the potentials directory of the LAMMPS -distribution have a ".edip" suffix. Lines that are not blank or -comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formula above: -

    -
    • element 1 (the center atom in a 3-body interaction) -
    • element 2 -
    • element 3 -
    • A (energy units) -
    • B (distance units) -
    • cutoffA (distance units) -
    • cutoffC (distance units) -
    • alpha -
    • beta -
    • eta -
    • gamma (distance units) -
    • lambda (energy units) -
    • mu -
    • tho -
    • sigma (distance units) -
    • Q0 -
    • u1 -
    • u2 -
    • u3 -
    • u4 -
    -

    The A, B, beta, sigma parameters are used only for two-body interactions. -The eta, gamma, lambda, mu, Q0 and all u1 to u4 parameters are used only -for three-body interactions. The alpha and cutoffC parameters are used -for the coordination environment function only. -

    -

    The EDIP potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. -

    -

    For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify EDIP parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. -

    -

    At the moment, only a single element parametrization is -implemented. However, the author is not aware of other -multi-element EDIP parametrizations. If you know any and -you are interest in that, please contact the author of -the EDIP package. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS -section for more info on packages. -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    The EDIP potential files provided with LAMMPS (see the potentials directory) -are parameterized for metal units. -You can use the SW potential with any LAMMPS units, but you would need -to create your own EDIP potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (EDIP) J. F. Justo et al., Phys. Rev. B 58, 2539 (1998). -

    - diff --git a/doc/doc2/pair_eff.html b/doc/doc2/pair_eff.html deleted file mode 100644 index 1e3b5391c5..0000000000 --- a/doc/doc2/pair_eff.html +++ /dev/null @@ -1,325 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style eff/cut command -

    -

    Syntax: -

    -
    pair_style eff/cut cutoff keyword args ... 
-
    -
    • cutoff = global cutoff for Coulombic interactions - -
    • zero or more keyword/value pairs may be appended - -
      keyword = limit/eradius or pressure/evirials or ecp
-  limit/eradius args = none
-  pressure/evirials args = none
-  ecp args = type element type element ...
-    type = LAMMPS atom type (1 to Ntypes)
-    element = element symbol (e.g. H, Si) 
-
      - -
    -

    Examples: -

    -
    pair_style eff/cut 39.7
-pair_style eff/cut 40.0 limit/eradius
-pair_style eff/cut 40.0 limit/eradius pressure/evirials
-pair_style eff/cut 40.0 ecp 1 Si 3 C
-pair_coeff * *
-pair_coeff 2 2 20.0
-pair_coeff 1 s 0.320852 2.283269 0.814857 
-pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 
-
    -

    Description: -

    -

    This pair style contains a LAMMPS implementation of the electron Force -Field (eFF) potential currently under development at Caltech, as -described in (Jaramillo-Botero). The eFF for Z<6 -was first introduced by (Su) in 2007. It has been extended to -higher Zs by using effective core potentials (ECPs) that now cover up -to 2nd and 3rd row p-block elements of the periodic table. -

    -

    eFF can be viewed as an approximation to QM wave packet dynamics and -Fermionic molecular dynamics, combining the ability of electronic -structure methods to describe atomic structure, bonding, and chemistry -in materials, and of plasma methods to describe nonequilibrium -dynamics of large systems with a large number of highly excited -electrons. Yet, eFF relies on a simplification of the electronic -wavefunction in which electrons are described as floating Gaussian -wave packets whose position and size respond to the various dynamic -forces between interacting classical nuclear particles and spherical -Gaussian electron wavepackets. The wavefunction is taken to be a -Hartree product of the wave packets. To compensate for the lack of -explicit antisymmetry in the resulting wavefunction, a spin-dependent -Pauli potential is included in the Hamiltonian. Substituting this -wavefunction into the time-dependent Schrodinger equation produces -equations of motion that correspond - to second order - to classical -Hamiltonian relations between electron position and size, and their -conjugate momenta. The N-electron wavefunction is described as a -product of one-electron Gaussian functions, whose size is a dynamical -variable and whose position is not constrained to a nuclear -center. This form allows for straightforward propagation of the -wavefunction, with time, using a simple formulation from which the -equations of motion are then integrated with conventional MD -algorithms. In addition to this spin-dependent Pauli repulsion -potential term between Gaussians, eFF includes the electron kinetic -energy from the Gaussians. These two terms are based on -first-principles quantum mechanics. On the other hand, nuclei are -described as point charges, which interact with other nuclei and -electrons through standard electrostatic potential forms. -

    -

    The full Hamiltonian (shown below), contains then a standard -description for electrostatic interactions between a set of -delocalized point and Gaussian charges which include, nuclei-nuclei -(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a -mixed QM-classical mechanics method rather than a conventional force -field method (in which electron motions are averaged out into ground -state nuclear motions, i.e a single electronic state, and particle -interactions are described via empirically parameterized interatomic -potential functions). This makes eFF uniquely suited to simulate -materials over a wide range of temperatures and pressures where -electronically excited and ionized states of matter can occur and -coexist. Furthermore, the interactions between particles -nuclei and -electrons- reduce to the sum of a set of effective pairwise potentials -in the eFF formulation. The eff/cut style computes the pairwise -Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee), -and the quantum-derived Pauli (E_PR) and Kinetic energy interactions -potentials between electrons (E_KE) for a total energy expression -given as, -

    -
    -
    -

    The individual terms are defined as follows: -

    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -

    where, s_i correspond to the electron sizes, the sigmas i's to the -fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij -to the distances between the nuclei or the nuclei and electrons, and -r_ij to the distances between electrons. For additional details see -(Jaramillo-Botero). -

    -

    The overall electrostatics energy is given in Hartree units of energy -by default and can be modified by an energy-conversion constant, -according to the units chosen (see electron_units). The -cutoff Rc, given in Bohrs (by default), truncates the interaction -distance. The recommended cutoff for this pair style should follow -the minimum image criterion, i.e. half of the minimum unit cell -length. -

    -

    Style eff/long (not yet available) computes the same interactions as -style eff/cut except that an additional damping factor is applied so -it can be used in conjunction with the -kspace_style command and its ewald or pppm -option. The Coulombic cutoff specified for this style means that -pairwise interactions within this distance are computed directly; -interactions outside that distance are computed in reciprocal space. -

    -

    This potential is designed to be used with atom_style -electron definitions, in order to handle the -description of systems with interacting nuclei and explicit electrons. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • cutoff (distance units) -
    -

    For eff/cut, the cutoff coefficient is optional. If it is not used -(as in some of the examples above), the default global value specified -in the pair_style command is used. -

    -

    For eff/long (not yet available) no cutoff will be specified for an -individual I,J type pair via the pair_coeff command. -All type pairs use the same global cutoff specified in the pair_style -command. -

    -
    - -

    The limit/eradius and pressure/evirials keywrods are optional. -Neither or both must be specified. If not specified they are unset. -

    -

    The limit/eradius keyword is used to restrain electron size from -becoming excessively diffuse at very high temperatures were the -Gaussian wave packet representation breaks down, and from expanding as -free particles to infinite size. If unset, electron radius is free to -increase without bounds. If set, a restraining harmonic potential of -the form E = 1/2k_ss^2 for s > L_box/2, where k_s = 1 Hartrees/Bohr^2, -is applied on the electron radius. -

    -

    The pressure/evirials keyword is used to control between two types -of pressure computation: if unset, the computed pressure does not -include the electronic radial virials contributions to the total -pressure (scalar or tensor). If set, the computed pressure will -include the electronic radial virial contributions to the total -pressure (scalar and tensor). -

    -

    The ecp keyword is used to associate an ECP representation for a -particular atom type. The ECP captures the orbital overlap between a -core pseudo particle and valence electrons within the Pauli repulsion. -A list of type:element-symbol pairs may be provided for all ECP -representations, after the "ecp" keyword. -

    -

    IMPORTANT NOTE: Default ECP parameters are provided for C, N, O, Al, -and Si. Users can modify these using the pair_coeff command as -exemplified above. For this, the User must distinguish between two -different functional forms supported, one that captures the orbital -overlap assuming the s-type core interacts with an s-like valence -electron (s-s) and another that assumes the interaction is s-p. For -systems that exhibit significant p-character (e.g. C, N, O) the s-p -form is recommended. The "s" ECP form requires 3 parameters and the -"p" 5 parameters. -

    -

    IMPORTANT NOTE: there are two different pressures that can be reported -for eFF when defining this pair_style, one (default) that considers -electrons do not contribute radial virial components (i.e. electrons -treated as incompressible 'rigid' spheres) and one that does. The -radial electronic contributions to the virials are only tallied if the -flexible pressure option is set, and this will affect both global and -per-atom quantities. In principle, the true pressure of a system is -somewhere in between the rigid and the flexible eFF pressures, but, -for most cases, the difference between these two pressures will not be -significant over long-term averaged runs (i.e. even though the energy -partitioning changes, the total energy remains similar). -

    -
    - -

    IMPORTANT NOTE: This implemention of eFF gives a reasonably accurate -description for systems containing nuclei from Z = 1-6 in "all -electron" representations. For systems with increasingly -non-spherical electrons, Users should use the ECP representations. -ECPs are now supported and validated for most of the 2nd and 3rd row -elements of the p-block. Predefined parameters are provided for C, N, -O, Al, and Si. The ECP captures the orbital overlap between the core -and valence electrons (i.e. Pauli repulsion) with one of the -functional forms: -

    -
    -
    -
    -
    -

    Where the 1st form correspond to core interactions with s-type valence -electrons and the 2nd to core interactions with p-type valence -electrons. -

    -

    The current version adds full support for models with fixed-core and -ECP definitions. to enable larger timesteps (i.e. by avoiding the -high frequency vibrational modes -translational and radial- of the 2 s -electrons), and in the ECP case to reduce the increased orbital -complexity in higher Z elements (up to Z<18). A fixed-core should be -defined with a mass that includes the corresponding nuclear mass plus -the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a -radius equivalent to that of minimized 1s electrons (see examples -under /examples/USER/eff/fixed-core). An pseudo-core should be -described with a mass that includes the corresponding nuclear mass, -plus all the core electrons (i.e no outer shell electrons), and a -radius equivalent to that of a corresponding minimized full-electron -system. The charge for a pseudo-core atom should be given by the -number of outer shell electrons. -

    -

    In general, eFF excels at computing the properties of materials in -extreme conditions and tracing the system dynamics over multi-picosend -timescales; this is particularly relevant where electron excitations -can change significantly the nature of bonding in the system. It can -capture with surprising accuracy the behavior of such systems because -it describes consistently and in an unbiased manner many different -kinds of bonds, including covalent, ionic, multicenter, ionic, and -plasma, and how they interconvert and/or change when they become -excited. eFF also excels in computing the relative thermochemistry of -isodemic reactions and conformational changes, where the bonds of the -reactants are of the same type as the bonds of the products. eFF -assumes that kinetic energy differences dominate the overall exchange -energy, which is true when the electrons present are nearly spherical -and nodeless and valid for covalent compounds such as dense hydrogen, -hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth -metals (e.g. beryllium) and semimetals such as boron; and various -compounds containing ionic and/or multicenter bonds, such as boron -dihydride. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the cutoff distance for the -eff/cut style can be mixed. The default mix value is geometric. -See the "pair_modify" command for details. -

    -

    The pair_modify shift option is not relevant for -these pair styles. -

    -

    The eff/long (not yet available) style supports the -pair_modify table option for tabulation of the -short-range portion of the long-range Coulombic interaction. -

    -

    These pair styles do not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    These pair styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    These pair styles will only be enabled if LAMMPS is built with the -USER-EFF package. It will only be enabled if LAMMPS was built with -that package. See the Making LAMMPS -section for more info. -

    -

    These pair styles require that particles store electron attributes -such as radius, radial velocity, and radital force, as defined by the -atom_style. The electron atom style does all of -this. -

    -

    Thes pair styles require you to use the comm_modify vel -yes command so that velocites are stored by ghost -atoms. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: -

    -

    If not specified, limit_eradius = 0 and pressure_with_evirials = 0. -

    -
    - - - -

    (Su) Su and Goddard, Excited Electron Dynamics Modeling of Warm -Dense Matter, Phys Rev Lett, 99:185003 (2007). -

    - - -

    (Jaramillo-Botero) Jaramillo-Botero, Su, Qi, Goddard, Large-scale, -Long-term Non-adiabatic Electron Molecular Dynamics for Describing -Material Properties and Phenomena in Extreme Environments, J Comp -Chem, 32, 497-512 (2011). -

    - diff --git a/doc/doc2/pair_eim.html b/doc/doc2/pair_eim.html deleted file mode 100644 index 01867a598e..0000000000 --- a/doc/doc2/pair_eim.html +++ /dev/null @@ -1,181 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style eim command -

    -

    pair_style eim/omp command -

    -

    Syntax: -

    -
    pair_style style 
-
    -
    • style = eim -
    -

    Examples: -

    -
    pair_style eim
-pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
-pair_coeff * * Na Cl ffield.eim  Na Na Na Cl
-pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na 
-
    -

    Description: -

    -

    Style eim computes pairwise interactions for ionic compounds -using embedded-ion method (EIM) potentials (Zhou). The -energy of the system E is given by -

    -
    -
    -

    The first term is a double pairwise sum over the J neighbors of all I -atoms, where phi_ij is a pair potential. The second term sums over -the embedding energy E_i of atom I, which is a function of its charge -q_i and the electrical potential sigma_i at its location. E_i, q_i, -and sigma_i are calculated as -

    -
    -
    -

    where eta_ji is a pairwise function describing electron flow from atom -I to atom J, and psi_ij is another pairwise function. The multi-body -nature of the EIM potential is a result of the embedding energy term. -A complete list of all the pair functions used in EIM is summarized -below -

    -
    -
    -

    Here E_b, r_e, r_(c,phi), alpha, beta, A_(psi), zeta, r_(s,psi), -r_(c,psi), A_(eta), r_(s,eta), r_(c,eta), chi, and pair function type -p are parameters, with subscripts ij indicating the two species of -atoms in the atomic pair. -

    -

    IMPORTANT NOTE: Even though the EIM potential is treating atoms as -charged ions, you should not use a LAMMPS atom_style -that stores a charge on each atom and thus requires you to assign a -charge to each atom, e.g. the charge or full atom styles. This is -because the EIM potential infers the charge on an atom from the -equation above for q_i; you do not assign charges explicitly. -

    -
    - -

    All the EIM parameters are listed in a potential file which is -specified by the pair_coeff command. This is an -ASCII text file in a format described below. The "ffield.eim" file -included in the "potentials" directory of the LAMMPS distribution -currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I. -A system with any combination of these elements can be modeled. This -file is parameterized in terms of LAMMPS metal units. -

    -

    Note that unlike other potentials, cutoffs for EIM potentials are not -set in the pair_style or pair_coeff command; they are specified in the -EIM potential file itself. Likewise, the EIM potential file lists -atomic masses; thus you do not need to use the mass -command to specify them. -

    -

    Only a single pair_coeff command is used with the eim style which -specifies an EIM potential file and the element(s) to extract -information for. The EIM elements are mapped to LAMMPS atom types by -specifying N additional arguments after the filename in the pair_coeff -command, where N is the number of LAMMPS atom types: -

    -
    • Elem1, Elem2, ... -
    • EIM potential file -
    • N element names = mapping of EIM elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example like one of those above, suppose you want to model a -system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms -types and you want the 1st 3 to be Na, and the 4th to be Cl, you would -use the following pair_coeff command: -

    -
    pair_coeff * * Na Cl ffield.eim Na Na Na Cl 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The filename is the EIM potential file. The Na and Cl arguments -(before the file name) are the two elements for which info will be -extracted from the potentail file. The first three trailing Na -arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The -final Cl argument maps LAMMPS atom type 4 to the EIM Cl element. -

    -

    If a mapping value is specified as NULL, the mapping is not performed. -This can be used when an eim potential is used as part of the -hybrid pair style. The NULL values are placeholders for atom types -that will be used with other potentials. -

    -

    The ffield.eim file in the potentials directory of the LAMMPS -distribution is formated as follows: -

    -

    Lines starting with # are comments and are ignored by LAMMPS. Lines -starting with "global:" include three global values. The first value -divides the cations from anions, i.e., any elements with -electronegativity above this value are viewed as anions, and any -elements with electronegativity below this value are viewed as -cations. The second and third values are related to the cutoff -function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above -equation can be derived from these values. -

    -

    Lines starting with "element:" are formatted as follows: name of -element, atomic number, atomic mass, electronic negativity, atomic -radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive -energy (LAMMPS ignores it), and q0 (must be 0). -

    -

    Lines starting with "pair:" are entered as: element 1, element 2, -r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e, -alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta, -r_(s,psi), and p. -

    -

    The lines in the file can be in any order; LAMMPS extracts the info it -needs. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package (which it is by default). -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Zhou) Zhou, submitted for publication (2010). Please contact -Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov. -

    - diff --git a/doc/doc2/pair_gauss.html b/doc/doc2/pair_gauss.html deleted file mode 100644 index a3753aab3c..0000000000 --- a/doc/doc2/pair_gauss.html +++ /dev/null @@ -1,172 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style gauss command -

    -

    pair_style gauss/gpu command -

    -

    pair_style gauss/omp command -

    -

    pair_style gauss/cut command -

    -

    pair_style gauss/cut/omp command -

    -

    Syntax: -

    -
    pair_style gauss cutoff
-pair_style gauss/cut cutoff 
-
    -
    • cutoff = global cutoff for Gauss interactions (distance units) -
    -

    Examples: -

    -
    pair_style gauss 12.0 
-pair_coeff * * 1.0 0.9
-pair_coeff 1 4 1.0 0.9 10.0 
-
    -
    pair_style gauss/cut 3.5
-pair_coeff 1 4 0.2805 1.45 0.112 
-
    -

    Description: -

    -

    Style gauss computes a tethering potential of the form -

    -
    -
    -

    between an atom and its corresponding tether site which will typically -be a frozen atom in the simulation. Rc is the cutoff. -

    -

    The following coefficients must be defined for each pair of atom types -via the pair_coeff command as in the examples above, -or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • A (energy units) -
    • B (1/distance^2 units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global cutoff -is used. -

    -

    Style gauss/cut computes a generalized Gaussian interaction potential -between pairs of particles: -

    -
    -
    -

    where H determines together with the standard deviation sigma_h the -peak height of the Gaussian function, and r_mh the peak position. -Examples of the use of the Gaussian potentials include implicit -solvent simulations of salt ions (Lenart) and of surfactants -(Jusufi). In these instances the Gaussian potential mimics -the hydration barrier between a pair of particles. The hydration -barrier is located at r_mh and has a width of sigma_h. The prefactor -determines the hight of the potential barrier. -

    -

    The following coefficients must be defined for each pair of atom types -via the pair_coeff command as in the example above, -or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • H (energy * distance units) -
    • r_mh (distance units) -
    • sigma_h (distance units) -
    -

    The global cutoff (r_c) specified in the pair_style command is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    The gauss style does not support the pair_modify -shift option. There is no effect due to the Gaussian well beyond the -cutoff; hence reasonable cutoffs need to be specified. -

    -

    The gauss/cut style supports the pair_modify shift -option for the energy of the Gauss-potential portion of the pair -interaction. -

    -

    The pair_modify table and tail options are not -relevant for these pair styles. -

    -

    These pair styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -

    The gauss pair style tallies an "occupancy" count of how many Gaussian-well -sites have an atom within the distance at which the force is a maximum -= sqrt(0.5/b). This quantity can be accessed via the compute -pair command as a vector of values of length 1. -

    -

    To print this quantity to the log file (with a descriptive column -heading) the following commands could be included in an input script: -

    -
    compute gauss all pair gauss
-variable occ equal c_gauss[1]
-thermo_style custom step temp epair v_occ 
-
    -
    - -

    Restrictions: -

    -

    The gauss/cut style is part of the "user-misc" package. It is only -enabled if LAMMPS is build with that package. See the Making of -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, -pair_style coul/diel -

    -

    Default: none -

    - - -

    (Lenart) Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, -044509 (2007). -

    - - -

    (Jusufi) Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, -13783 (2008). -

    - diff --git a/doc/doc2/pair_gayberne.html b/doc/doc2/pair_gayberne.html deleted file mode 100644 index 27de230530..0000000000 --- a/doc/doc2/pair_gayberne.html +++ /dev/null @@ -1,243 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style gayberne command -

    -

    pair_style gayberne/gpu command -

    -

    pair_style gayberne/intel command -

    -

    pair_style gayberne/omp command -

    -

    Syntax: -

    -
    pair_style gayberne gamma upsilon mu cutoff 
-
    -
    • gamma = shift for potential minimum (typically 1) -
    • upsilon = exponent for eta orientation-dependent energy function -
    • mu = exponent for chi orientation-dependent energy function -
    • cutoff = global cutoff for interactions (distance units) -
    -

    Examples: -

    -
    pair_style gayberne 1.0 1.0 1.0 10.0
-pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 
-
    -

    Description: -

    -

    The gayberne styles compute a Gay-Berne anisotropic LJ interaction -(Berardi) between pairs of ellipsoidal particles or an -ellipsoidal and spherical particle via the formulas -

    -
    -
    -

    where A1 and A2 are the transformation matrices from the simulation -box frame to the body frame and r12 is the center to center vector -between the particles. Ur controls the shifted distance dependent -interaction based on the distance of closest approach of the two -particles (h12) and the user-specified shift parameter gamma. When -both particles are spherical, the formula reduces to the usual -Lennard-Jones interaction (see details below for when Gay-Berne treats -a particle as "spherical"). -

    -

    For large uniform molecules it has been shown that the energy -parameters are approximately representable in terms of local contact -curvatures (Everaers): -

    -
    -
    -

    The variable names utilized as potential parameters are for the most -part taken from (Everaers) in order to be consistent with -the RE-squared pair potential. Details on the -upsilon and mu parameters are given -here. -

    -

    More details of the Gay-Berne formulation are given in the references -listed below and in this supplementary -document. -

    -

    Use of this pair style requires the NVE, NVT, or NPT fixes with the -asphere extension (e.g. fix nve/asphere) in -order to integrate particle rotation. Additionally, atom_style -ellipsoid should be used since it defines the -rotational state and the size and shape of each ellipsoidal particle. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon = well depth (energy units) -
    • sigma = minimum effective particle radii (distance units) -
    • epsilon_i_a = relative well depth of type I for side-to-side interactions -
    • epsilon_i_b = relative well depth of type I for face-to-face interactions -
    • epsilon_i_c = relative well depth of type I for end-to-end interactions -
    • epsilon_j_a = relative well depth of type J for side-to-side interactions -
    • epsilon_j_b = relative well depth of type J for face-to-face interactions -
    • epsilon_j_c = relative well depth of type J for end-to-end interactions -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global -cutoff specified in the pair_style command is used. -

    -

    It is typical with the Gay-Berne potential to define sigma as the -minimum of the 3 shape diameters of the particles involved in an I,I -interaction, though this is not required. Note that this is a -different meaning for sigma than the pair_style -resquared potential uses. -

    -

    The epsilon_i and epsilon_j coefficients are actually defined for atom -types, not for pairs of atom types. Thus, in a series of pair_coeff -commands, they only need to be specified once for each atom type. -

    -

    Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are -non-zero, the three values are assigned to atom type I. If all the -epsilon_i values are zero, they are ignored. If any of epsilon_j_a, -epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned -to atom type J. If all three epsilon_j values are zero, they are -ignored. Thus the typical way to define the epsilon_i and epsilon_j -coefficients is to list their values in "pair_coeff I J" commands when -I = J, but set them to 0.0 when I != J. If you do list them when I != -J, you should insure they are consistent with their values in other -pair_coeff commands, since only the last setting will be in effect. -

    -

    Note that if this potential is being used as a sub-style of -pair_style hybrid, and there is no "pair_coeff I I" -setting made for Gay-Berne for a particular type I (because I-I -interactions are computed by another hybrid pair potential), then you -still need to insure the epsilon a,b,c coefficients are assigned to -that type. e.g. in a "pair_coeff I J" command. -

    -

    IMPORTANT NOTE: If the epsilon a = b = c for an atom type, and if the -shape of the particle itself is spherical, meaning its 3 shape -parameters are all the same, then the particle is treated as an LJ -sphere by the Gay-Berne potential. This is significant because if two -LJ spheres interact, then the simple Lennard-Jones formula is used to -compute their interaction energy/force using the specified epsilon and -sigma as the standard LJ parameters. This is much cheaper to compute -than the full Gay-Berne formula. To treat the particle as a LJ sphere -with sigma = D, you should normally set epsilon a = b = c = 1.0, set -the pair_coeff sigma = D, and also set the 3 shape parameters for the -particle to D. The one exception is that if the 3 shape parameters -are set to 0.0, which is a valid way in LAMMPS to specify a point -particle, then the Gay-Berne potential will treat that as shape -parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it -requires finite-size particles. In this case you should still set the -pair_coeff sigma to 1.0 as well. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for this pair style can be mixed. The default mix -value is geometric. See the "pair_modify" command for details. -

    -

    This pair styles supports the pair_modify shift -option for the energy of the Lennard-Jones portion of the pair -interaction, but only for sphere-sphere interactions. There is no -shifting performed for ellipsoidal interactions due to the anisotropic -dependence of the interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    The gayberne style is part of the ASPHERE package. It is only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    These pair style require that atoms store torque and a quaternion to -represent their orientation, as defined by the -atom_style. It also require they store a per-type -shape. The particles cannot store a per-particle -diameter. -

    -

    This pair style requires that atoms be ellipsoids as defined by the -atom_style ellipsoid command. -

    -

    Particles acted on by the potential can be finite-size aspherical or -spherical particles, or point particles. Spherical particles have all -3 of their shape parameters equal to each other. Point particles have -all 3 of their shape parameters equal to 0.0. -

    -

    The Gay-Berne potential does not become isotropic as r increases -(Everaers). The distance-of-closest-approach -approximation used by LAMMPS becomes less accurate when high-aspect -ratio ellipsoids are used. -

    -

    Related commands: -

    -

    pair_coeff, fix nve/asphere, -compute temp/asphere, pair_style -resquared -

    -

    Default: none -

    -
    - - - -

    (Everaers) Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). -

    - - -

    (Berardi) Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). -Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008). -

    - - -

    (Perram) Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996). -

    - - -

    (Allen) Allen and Germano, Mol Phys 104, 3225-3235 (2006). -

    - diff --git a/doc/doc2/pair_gran.html b/doc/doc2/pair_gran.html deleted file mode 100644 index 281d2246e7..0000000000 --- a/doc/doc2/pair_gran.html +++ /dev/null @@ -1,279 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style gran/hooke command -

    -

    pair_style gran/cuda command -

    -

    pair_style gran/omp command -

    -

    pair_style gran/hooke/history command -

    -

    pair_style gran/hooke/history/omp command -

    -

    pair_style gran/hertz/history command -

    -

    pair_style gran/hertz/history/omp command -

    -

    Syntax: -

    -
    pair_style style Kn Kt gamma_n gamma_t xmu dampflag 
-
    -
    • style = gran/hooke or gran/hooke/history or gran/hertz/history - -
    • Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) - -
    • Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) - -
    • gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) - -
    • gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) - -
    • xmu = static yield criterion (unitless value between 0.0 and 1.0e4) - -
    • dampflag = 0 or 1 if tangential damping force is excluded or included -
    -

    IMPORTANT NOTE: Versions of LAMMPS before 9Jan09 had different style -names for granular force fields. This is to emphasize the fact that -the Hertzian equation has changed to model polydispersity more -accurately. A side effect of the change is that the Kn, Kt, gamma_n, -and gamma_t coefficients in the pair_style command must be specified -with different values in order to reproduce calculations made with -earlier versions of LAMMPS, even for monodisperse systems. See the -NOTE below for details. -

    -

    Examples: -

    -
    pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
-pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 
-
    -

    Description: -

    -

    The gran styles use the following formulas for the frictional force -between two granular particles, as described in -(Brilliantov), (Silbert), and -(Zhang), when the distance r between two particles of radii -Ri and Rj is less than their contact distance d = Ri + Rj. There is -no force between the particles when r > d. -

    -

    The two Hookean styles use this formula: -

    -
    -
    -

    The Hertzian style uses this formula: -

    -
    -
    -

    In both equations the first parenthesized term is the normal force -between the two particles and the second parenthesized term is the -tangential force. The normal force has 2 terms, a contact force and a -damping force. The tangential force also has 2 terms: a shear force -and a damping force. The shear force is a "history" effect that -accounts for the tangential displacement between the particles for the -duration of the time they are in contact. This term is included in -pair styles hooke/history and hertz/history, but is not included -in pair style hooke. The tangential damping force term is included -in all three pair styles if dampflag is set to 1; it is not included -if dampflag is set to 0. -

    -

    The other quantities in the equations are as follows: -

    -
    • delta = d - r = overlap distance of 2 particles -
    • Kn = elastic constant for normal contact -
    • Kt = elastic constant for tangential contact -
    • gamma_n = viscoelastic damping constant for normal contact -
    • gamma_t = viscoelastic damping constant for tangential contact -
    • m_eff = Mi Mj / (Mi + Mj) = effective mass of 2 particles of mass Mi and Mj -
    • Delta St = tangential displacement vector between 2 spherical particles which is truncated to satisfy a frictional yield criterion -
    • n_ij = unit vector along the line connecting the centers of the 2 particles -
    • Vn = normal component of the relative velocity of the 2 particles -
    • Vt = tangential component of the relative velocity of the 2 particles -
    -

    The Kn, Kt, gamma_n, and gamma_t coefficients are specified as -parameters to the pair_style command. If a NULL is used for Kt, then -a default value is used where Kt = 2/7 Kn. If a NULL is used for -gamma_t, then a default value is used where gamma_t = 1/2 gamma_n. -

    -

    The interpretation and units for these 4 coefficients are different in -the Hookean versus Hertzian equations. -

    -

    The Hookean model is one where the normal push-back force for two -overlapping particles is a linear function of the overlap distance. -Thus the specified Kn is in units of (force/distance). Note that this -push-back force is independent of absolute particle size (in the -monodisperse case) and of the relative sizes of the two particles (in -the polydisperse case). This model also applies to the other terms in -the force equation so that the specified gamma_n is in units of -(1/time), Kt is in units of (force/distance), and gamma_t is in units -of (1/time). -

    -

    The Hertzian model is one where the normal push-back force for two -overlapping particles is proportional to the area of overlap of the -two particles, and is thus a non-linear function of overlap distance. -Thus Kn has units of force per area and is thus specified in units of -(pressure). The effects of absolute particle size (monodispersity) -and relative size (polydispersity) are captured in the radii-dependent -pre-factors. When these pre-factors are carried through to the other -terms in the force equation it means that the specified gamma_n is in -units of (1/(time*distance)), Kt is in units of (pressure), and -gamma_t is in units of (1/(time*distance)). -

    -

    Note that in the Hookean case, Kn can be thought of as a linear spring -constant with units of force/distance. In the Hertzian case, Kn is -like a non-linear spring constant with units of force/area or -pressure, and as shown in the (Zhang) paper, Kn = 4G / -(3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E / -(2(1+nu)), and E = Young's modulus. Similarly, Kt = 4G / (2-nu). -(NOTE: in an earlier version of the manual, we incorrectly stated that -Kt = 8G / (2-nu).) -

    -

    Thus in the Hertzian case Kn and Kt can be set to values that -corresponds to properties of the material being modeled. This is also -true in the Hookean case, except that a spring constant must be chosen -that is appropriate for the absolute size of particles in the model. -Since relative particle sizes are not accounted for, the Hookean -styles may not be a suitable model for polydisperse systems. -

    -

    IMPORTANT NOTE: In versions of LAMMPS before 9Jan09, the equation for -Hertzian interactions did not include the sqrt(RiRj/Ri+Rj) term and -thus was not as accurate for polydisperse systems. For monodisperse -systems, sqrt(RiRj/Ri+Rj) is a constant factor that effectively scales -all 4 coefficients: Kn, Kt, gamma_n, gamma_t. Thus you can set the -values of these 4 coefficients appropriately in the current code to -reproduce the results of a previous Hertzian monodisperse calculation. -For example, for the common case of a monodisperse system with -particles of diameter 1, all 4 of these coefficients should now be set -2x larger than they were previously. -

    -

    Xmu is also specified in the pair_style command and is the upper limit -of the tangential force through the Coulomb criterion Ft = xmu*Fn, -where Ft and Fn are the total tangential and normal force components -in the formulas above. Thus in the Hookean case, the tangential force -between 2 particles grows according to a tangential spring and -dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until -the particles lose contact. In the Hertzian case, a similar analogy -holds, though the spring is no longer linear. -

    -

    IMPORTANT NOTE: Normally, xmu should be specified as a fractional -value between 0.0 and 1.0, however LAMMPS allows large values (up to -1.0e4) to allow for modeling of systems which can sustain very large -tangential forces. -

    -

    For granular styles there are no additional coefficients to set for -each pair of atom types via the pair_coeff command. -All settings are global and are made via the pair_style command. -However you must still use the pair_coeff for all -pairs of granular atom types. For example the command -

    -
    pair_coeff * * 
-
    -

    should be used if all atoms in the simulation interact via a granular -potential (i.e. one of the pair styles above is used). If a granular -potential is used as a sub-style of pair_style -hybrid, then specific atom types can be used in the -pair_coeff command to determine which atoms interact via a granular -potential. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    The pair_modify mix, shift, table, and tail options -are not relevant for granular pair styles. -

    -

    These pair styles write their information to binary restart -files, so a pair_style command does not need to be -specified in an input script that reads a restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -

    The single() function of these pair styles returns 0.0 for the energy -of a pairwise interaction, since energy is not conserved in these -dissipative potentials. It also returns only the normal component of -the pairwise interaction force. However, the single() function also -calculates 4 extra pairwise quantities. The first 3 are the -components of the tangential force between particles I and J, acting -on particle I. P4 is the magnitude of this tangential force. These -extra quantites can be accessed by the compute -pair/local command, as p1, p2, p3, -p4. -

    -
    - -

    Restrictions: none -

    -

    All the granular pair styles are part of the GRANULAR package. It is -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    These pair styles require that atoms store torque and angular velocity -(omega) as defined by the atom_style. They also -require a per-particle radius is stored. The sphere atom style does -all of this. -

    -

    This pair style requires you to use the comm_modify vel -yes command so that velocites are stored by ghost -atoms. -

    -

    These pair styles will not restart exactly when using the -read_restart command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -read_restart command for more details. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Brilliantov) Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53, -p 5382-5392 (1996). -

    - - -

    (Silbert) Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev -E, 64, p 051302 (2001). -

    - - -

    (Zhang) Zhang and Makse, Phys Rev E, 72, p 011301 (2005). -

    - diff --git a/doc/doc2/pair_gromacs.html b/doc/doc2/pair_gromacs.html deleted file mode 100644 index eb74024b82..0000000000 --- a/doc/doc2/pair_gromacs.html +++ /dev/null @@ -1,170 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/gromacs command -

    -

    pair_style lj/gromacs/cuda command -

    -

    pair_style lj/gromacs/gpu command -

    -

    pair_style lj/gromacs/omp command -

    -

    pair_style lj/gromacs/coul/gromacs command -

    -

    pair_style lj/gromacs/coul/gromacs/cuda command -

    -

    pair_style lj/gromacs/coul/gromacs/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = lj/gromacs or lj/gromacs/coul/gromacs -
    • args = list of arguments for a particular style -
    -
      lj/gromacs args = inner outer
-    inner, outer = global switching cutoffs for Lennard Jones
-  lj/gromacs/coul/gromacs args = inner outer (inner2) (outer2)
-    inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
-    inner2, outer2 = global switching cutoffs for Coulombic (optional) 
-
    -

    Examples: -

    -
    pair_style lj/gromacs 9.0 12.0
-pair_coeff * * 100.0 2.0
-pair_coeff 2 2 100.0 2.0 8.0 10.0 
-
    -
    pair_style lj/gromacs/coul/gromacs 9.0 12.0
-pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
-pair_coeff * * 100.0 2.0 
-
    -

    Description: -

    -

    The lj/gromacs styles compute shifted LJ and Coulombic interactions -with an additional switching function S(r) that ramps the energy and force -smoothly to zero between an inner and outer cutoff. It is a commonly -used potential in the GROMACS MD code and for -the coarse-grained models of (Marrink). -

    -
    -
    -

    r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B, -and C are computed by LAMMPS to perform the shifting and smoothing. -The function -S(r) is actually applied once to each term of the LJ formula and once -to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients -depending on which pair_style is used. The boundary conditions -applied to the smoothing function are as follows: S'(r1) = S''(r1) = 0, -S(rc) = -E(rc), S'(rc) = -E'(rc), and S''(rc) = -E''(rc), -where E(r) is the corresponding term -in the LJ or Coulombic potential energy function. -Single and double primes denote first and second -derivatives with respect to r, respectively. -

    -

    The inner and outer cutoff for the LJ and Coulombic terms can be the -same or different depending on whether 2 or 4 arguments are used in -the pair_style command. The inner LJ cutoff must be > 0, but the -inner Coulombic cutoff can be >= 0. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • inner (distance units) -
    • outer (distance units) -
    -

    Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. -

    -

    The last 2 coefficients are optional inner and outer cutoffs for style -lj/gromacs. If not specified, the global inner and outer values -are used. -

    -

    The last 2 coefficients cannot be used with style -lj/gromacs/coul/gromacs because this force field does not allow -varying cutoffs for individual atom pairs; all pairs use the global -cutoff(s) specified in the pair_style command. -

    -
    - -

    Styles intel, kk, with a cuda, gpu, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is geometric. See the "pair_modify" command -for details. -

    -

    None of the GROMACS pair styles support the -pair_modify shift option, since the Lennard-Jones -portion of the pair interaction is already smoothed to 0.0 at the -cutoff. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    None of the GROMACS pair styles support the -pair_modify tail option for adding long-range tail -corrections to energy and pressure, since there are no corrections for -a potential that goes to 0.0 at the cutoff. -

    -

    All of the GROMACS pair styles write their information to binary -restart files, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. -

    -

    All of the GROMACS pair styles can only be used via the pair -keyword of the run_style respa command. They do not -support the inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Marrink) Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004). -

    - diff --git a/doc/doc2/pair_hbond_dreiding.html b/doc/doc2/pair_hbond_dreiding.html deleted file mode 100644 index 617d0fa3fa..0000000000 --- a/doc/doc2/pair_hbond_dreiding.html +++ /dev/null @@ -1,255 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style hbond/dreiding/lj command -

    -

    pair_style hbond/dreiding/lj/omp command -

    -

    pair_style hbond/dreiding/morse command -

    -

    pair_style hbond/dreiding/morse/omp command -

    -

    Syntax: -

    -
    pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof 
-
    -
    • style = hbond/dreiding/lj or hbond/dreiding/morse -
    • n = cosine angle periodicity -
    • inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units) -
    • outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units) -
    • angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor -
    • interactions (degrees) -
    -

    Examples: -

    -
    pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
-pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 
-
    -
    pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
-pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 
-
    -

    Description: -

    -

    The hbond/dreiding styles compute the Acceptor-Hydrogen-Donor (AHD) -3-body hydrogen bond interaction for the -DREIDING force field, given by: -

    -
    -
    -

    where Rin is the inner spline distance cutoff, Rout is the outer -distance cutoff, theta_c is the angle cutoff, and n is the cosine -periodicity. -

    -

    Here, r is the radial distance between the donor (D) and acceptor -(A) atoms and theta is the bond angle between the acceptor, the -hydrogen (H) and the donor atoms: -

    -
    -
    -

    These 3-body interactions can be defined for pairs of acceptor and -donor atoms, based on atom types. For each donor/acceptor atom pair, -the 3rd atom in the interaction is a hydrogen permanently bonded to -the donor atom, e.g. in a bond list read in from a data file via the -read_data command. The atom types of possible -hydrogen atoms for each donor/acceptor type pair are specified by the -pair_coeff command (see below). -

    -

    Style hbond/dreiding/lj is the original DREIDING potential of -(Mayo). It uses a LJ 12/10 functional for the Donor-Acceptor -interactions. To match the results in the original paper, use n = 4. -

    -

    Style hbond/dreiding/morse is an improved version using a Morse -potential for the Donor-Acceptor interactions. (Liu) showed -that the Morse form gives improved results for Dendrimer simulations, -when n = 2. -

    -

    See this howto section of the manual for -more information on the DREIDING forcefield. -

    -

    IMPORTANT NOTE: Because the Dreiding hydrogen bond potential is only -one portion of an overall force field which typically includes other -pairwise interactions, it is common to use it as a sub-style in a -pair_style hybrid/overlay command, where another -pair style provides the repulsive core interaction between pairs of -atoms, e.g. a 1/r^12 Lennard-Jones repulsion. -

    -

    IMPORTANT NOTE: When using the hbond/dreiding pair styles with -pair_style hybrid/overlay, you should explicitly -define pair interactions between the donor atom and acceptor atoms, -(as well as between these atoms and ALL other atoms in your system). -Whenever pair_style hybrid/overlay is used, -ordinary mixing rules are not applied to atoms like the donor and -acceptor atoms because they are typically referenced in multiple pair -styles. Neglecting to do this can cause difficult-to-detect physics -problems. -

    -

    IMPORTANT NOTE: In the original Dreiding force field paper 1-4 -non-bonded interactions ARE allowed. If this is desired for your -model, use the special_bonds command (e.g. "special_bonds lj 0.0 0.0 -1.0") to turn these interactions on. -

    -
    - -

    The following coefficients must be defined for pairs of eligible -donor/acceptor types via the pair_coeff command as -in the examples above. -

    -

    IMPORTANT NOTE: Unlike other pair styles and their associated -pair_coeff commands, you do not need to specify -pair_coeff settings for all possible I,J type pairs. Only I,J type -pairs for atoms which act as joint donors/acceptors need to be -specified; all other type pairs are assumed to be inactive. -

    -

    IMPORTANT NOTE: A pair_coeff command can be -speficied multiple times for the same donor/acceptor type pair. This -enables multiple hydrogen types to be assigned to the same -donor/acceptor type pair. For other pair_styles, if the pair_coeff -command is re-used for the same I.J type pair, the settings for that -type pair are overwritten. For the hydrogen bond potentials this is -not the case; the settings are cummulative. This means the only way -to turn off a previous setting, is to re-use the pair_style command -and start over. -

    -

    For the hbond/dreiding/lj style the list of coefficients is as -follows: -

    -
    • K = hydrogen atom type = 1 to Ntypes -
    • donor flag = i or j -
    • epsilon (energy units) -
    • sigma (distance units) -
    • n = exponent in formula above -
    • distance cutoff Rin (distance units) -
    • distance cutoff Rout (distance units) -
    • angle cutoff (degrees) -
    -

    For the hbond/dreiding/morse style the list of coefficients is as -follows: -

    -
    • K = hydrogen atom type = 1 to Ntypes -
    • donor flag = i or j -
    • D0 (energy units) -
    • alpha (1/distance units) -
    • r0 (distance units) -
    • n = exponent in formula above -
    • distance cutoff Rin (distance units) -
    • distance cutoff Rout (distance units) -
    • angle cutoff (degrees) -
    -

    A single hydrogen atom type K can be specified, or a wild-card -asterisk can be used in place of or in conjunction with the K -arguments to select multiple types as hydrogens. This takes the form -"*" or "*n" or "n*" or "m*n". See the pair_coeff command -doc page for details. -

    -

    If the donor flag is i, then the atom of type I in the pair_coeff -command is treated as the donor, and J is the acceptor. If the donor -flag is j, then the atom of type J in the pair_coeff command is -treated as the donor and I is the donor. This option is required -because the pair_coeff command requires that I <= J. -

    -

    Epsilon and sigma are settings for the hydrogen bond potential based -on a Lennard-Jones functional form. Note that sigma is defined as the -zero-crossing distance for the potential, not as the energy minimum at -2^(1/6) sigma. -

    -

    D0 and alpha and r0 are settings for the hydrogen bond potential based -on a Morse functional form. -

    -

    The last 3 coefficients for both styles are optional. If not -specified, the global n, distance cutoff, and angle cutoff specified -in the pair_style command are used. If you wish to only override the -2nd or 3rd optional parameter, you must also specify the preceding -optional parameters. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support mixing. You must explicitly identify -each donor/acceptor type pair. -

    -

    These styles do not support the pair_modify shift -option for the energy of the interactions. -

    -

    The pair_modify table option is not relevant for -these pair styles. -

    -

    These pair styles do not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    These pair styles do not write their information to binary restart -files, so pair_style and pair_coeff commands need to be -re-specified in an input script that reads a restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -

    These pair styles tally a count of how many hydrogen bonding -interactions they calculate each timestep and the hbond energy. These -quantities can be accessed via the compute pair -command as a vector of values of length 2. -

    -

    To print these quantities to the log file (with a descriptive column -heading) the following commands could be included in an input script: -

    -
    compute hb all pair hbond/dreiding/lj
-variable n_hbond equal c_hb[1] #number hbonds
-variable E_hbond equal c_hb[2] #hbond energy
-thermo_style custom step temp epair v_E_hbond 
-
    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). -

    - - -

    (Liu) Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) -2798 (2009) -

    - diff --git a/doc/doc2/pair_hybrid.html b/doc/doc2/pair_hybrid.html deleted file mode 100644 index 9815d08fb0..0000000000 --- a/doc/doc2/pair_hybrid.html +++ /dev/null @@ -1,390 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style hybrid command -

    -

    pair_style hybrid/omp command -

    -

    pair_style hybrid/overlay command -

    -

    pair_style hybrid/overlay/omp command -

    -

    Syntax: -

    -
    pair_style hybrid style1 args style2 args ...
-pair_style hybrid/overlay style1 args style2 args ... 
-
    -
    • style1,style2 = list of one or more pair styles and their arguments -
    -

    Examples: -

    -
    pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
-pair_coeff 1*2 1*2 eam niu3
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.5 1.2 
-
    -
    pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff * * coul/long 
-
    -

    Description: -

    -

    The hybrid and hybrid/overlay styles enable the use of multiple -pair styles in one simulation. With the hybrid style, exactly one -pair style is assigned to each pair of atom types. With the -hybrid/overlay style, one or more pair styles can be assigned to -each pair of atom types. The assignment of pair styles to type pairs -is made via the pair_coeff command. -

    -

    Here are two examples of hybrid simulations. The hybrid style could -be used for a simulation of a metal droplet on a LJ surface. The -metal atoms interact with each other via an eam potential, the -surface atoms interact with each other via a lj/cut potential, and -the metal/surface interaction is also computed via a lj/cut -potential. The hybrid/overlay style could be used as in the 2nd -example above, where multiple potentials are superposed in an additive -fashion to compute the interaction between atoms. In this example, -using lj/cut and coul/long together gives the same result as if -the lj/cut/coul/long potential were used by itself. In this case, -it would be more efficient to use the single combined potential, but -in general any combination of pair potentials can be used together in -to produce an interaction that is not encoded in any single pair_style -file, e.g. adding Coulombic forces between granular particles. -

    -

    All pair styles that will be used are listed as "sub-styles" following -the hybrid or hybrid/overlay keyword, in any order. Each -sub-style's name is followed by its usual arguments, as illustrated in -the example above. See the doc pages of individual pair styles for a -listing and explanation of the appropriate arguments. -

    -

    Note that an individual pair style can be used multiple times as a -sub-style. For efficiency this should only be done if your model -requires it. E.g. if you have different regions of Si and C atoms and -wish to use a Tersoff potential for pure Si for one set of atoms, and -a Tersoff potetnial for pure C for the other set (presumably with some -3rd potential for Si-C interactions), then the sub-style tersoff -could be listed twice. But if you just want to use a Lennard-Jones or -other pairwise potential for several different atom type pairs in your -model, then you should just list the sub-style once and use the -pair_coeff command to assign parameters for the different type pairs. -

    -

    IMPORTANT NOTE: There are two exceptions to this option to list an -individual pair style multiple times. The first is for pair styles -implemented as Fortran libraries: pair_style meam and -pair_style reax (pair_style reax/c -is OK). This is because unlike a C++ class, they can not be -instantiated multiple times, due to the manner in which they were -coded in Fortran. The second is for GPU-enabled pair styles in the -GPU package. This is b/c the GPU package also currently assumes that -only one instance of a pair style is being used. -

    -

    In the pair_coeff commands, the name of a pair style must be added -after the I,J type specification, with the remaining coefficients -being those appropriate to that style. If the pair style is used -multiple times in the pair_style command, then an additional numeric -argument must also be specified which is a number from 1 to M where M -is the number of times the sub-style was listed in the pair style -command. The extra number indicates which instance of the sub-style -these coefficients apply to. -

    -

    For example, consider a simulation with 3 atom types: types 1 and 2 -are Ni atoms, type 3 are LJ atoms with charges. The following -commands would set up a hybrid simulation: -

    -
    pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
-pair_coeff * * eam/alloy nialhjea Ni Ni NULL
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.8 1.3 
-
    -

    As an example of using the same pair style multiple times, consider a -simulation with 2 atom types. Type 1 is Si, type 2 is C. The -following commands would model the Si atoms with Tersoff, the C atoms -with Tersoff, and the cross-interactions with Lennard-Jones: -

    -
    pair_style hybrid lj/cut 2.5 tersoff tersoff
-pair_coeff * * tersoff 1 Si.tersoff Si NULL 
-pair_coeff * * tersoff 2 C.tersoff NULL C
-pair_coeff 1 2 lj/cut 1.0 1.5 
-
    -

    If pair coefficients are specified in the data file read via the -read_data command, then the same rule applies. -E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for -each line in the "Pair Coeffs" section, e.g. -

    -
    Pair Coeffs 
-
    -
    1 lj/cut/coul/cut 1.0 1.0
-... 
-
    -

    Note that the pair_coeff command for some potentials such as -pair_style eam/alloy includes a mapping specification -of elements to all atom types, which in the hybrid case, can include -atom types not assigned to the eam/alloy potential. The NULL -keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO, -etc), to denote an atom type that will be assigned to a different -sub-style. -

    -

    For the hybrid style, each atom type pair I,J is assigned to exactly -one sub-style. Just as with a simulation using a single pair style, -if you specify the same atom type pair in a second pair_coeff command, -the previous assignment will be overwritten. -

    -

    For the hybrid/overlay style, each atom type pair I,J can be -assigned to one or more sub-styles. If you specify the same atom type -pair in a second pair_coeff command with a new sub-style, then the -second sub-style is added to the list of potentials that will be -calculated for two interacting atoms of those types. If you specify -the same atom type pair in a second pair_coeff command with a -sub-style that has already been defined for that pair of atoms, then -the new pair coefficients simply override the previous ones, as in the -normal usage of the pair_coeff command. E.g. these two sets of -commands are the same: -

    -
    pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 2 2 1.5 0.8 
-
    -
    pair_style hybrid/overlay lj/cut 2.5
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff 2 2 lj/cut 1.5 0.8 
-
    -

    Coefficients must be defined for each pair of atoms types via the -pair_coeff command as described above, or in the -data file or restart files read by the read_data or -read_restart commands, or by mixing as described -below. -

    -

    For both the hybrid and hybrid/overlay styles, every atom type -pair I,J (where I <= J) must be assigned to at least one sub-style via -the pair_coeff command as in the examples above, or -in the data file read by the read_data, or by mixing -as described below. -

    -

    If you want there to be no interactions between a particular pair of -atom types, you have 3 choices. You can assign the type pair to some -sub-style and use the neigh_modify exclude type -command. You can assign it to some sub-style and set the coefficients -so that there is effectively no interaction (e.g. epsilon = 0.0 in a -LJ potential). Or, for hybrid and hybrid/overlay simulations, you -can use this form of the pair_coeff command in your input script: -

    -
    pair_coeff	2 3 none 
-
    -

    or this form in the "Pair Coeffs" section of the data file: -

    -
    3 none 
-
    -

    If an assignment to none is made in a simulation with the -hybrid/overlay pair style, it wipes out all previous assignments of -that atom type pair to sub-styles. -

    -

    Note that you may need to use an atom_style hybrid -command in your input script, if atoms in the simulation will need -attributes from several atom styles, due to using multiple pair -potentials. -

    -
    - -

    Different force fields (e.g. CHARMM vs AMBER) may have different rules -for applying weightings that change the strength of pairwise -interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4 -neighbors in the molecular bond topology, as normally set by the -special_bonds command. Different weights can be -assigned to different pair hybrid sub-styles via the pair_modify -special command. This allows multiple force fields -to be used in a model of a hybrid system, however, there is no consistent -approach to determine parameters automatically for the interactions -between the two force fields, this is only recommended when particles -described by the different force fields do not mix. -

    -

    Here is an example for mixing CHARMM and AMBER: The global amber -setting sets the 1-4 interactions to non-zero scaling factors and -then overrides them with 0.0 only for CHARMM: -

    -
    special_bonds amber
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 
-
    -

    The this input achieves the same effect: -

    -
    special_bonds 0.0 0.0 0.1
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
-pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 
-
    -

    Here is an example for mixing Tersoff with OPLS/AA based on -a data file that defines bonds for all atoms where for the -Tersoff part of the system the force constants for the bonded -interactions have been set to 0. Note the global settings are -effectively lj/coul 0.0 0.0 0.5 as required for OPLS/AA: -

    -
    special_bonds lj/coul 1e-20 1e-20 0.5
-pair_hybrid tersoff lj/cut/coul/long 12.0
-pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 
-
    -

    See the pair_modify doc page for details on -the specific syntax, requirements and restrictions. -

    -
    - -

    The potential energy contribution to the overall system due to an -individual sub-style can be accessed and output via the compute -pair command. -

    -
    - -

    IMPORTANT: Several of the potentials defined via the pair_style -command in LAMMPS are really many-body potentials, such as Tersoff, -AIREBO, MEAM, ReaxFF, etc. The way to think about using these -potentials in a hybrid setting is as follows. -

    -

    A subset of atom types is assigned to the many-body potential with a -single pair_coeff command, using "* *" to include -all types and the NULL keywords described above to exclude specific -types not assigned to that potential. If types 1,3,4 were assigned in -that way (but not type 2), this means that all many-body interactions -between all atoms of types 1,3,4 will be computed by that potential. -Pair_style hybrid allows interactions between type pairs 2-2, 1-2, -2-3, 2-4 to be specified for computation by other pair styles. You -could even add a second interaction for 1-1 to be computed by another -pair style, assuming pair_style hybrid/overlay is used. -

    -

    But you should not, as a general rule, attempt to exclude the -many-body interactions for some subset of the type pairs within the -set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That -is not conceptually well-defined for many-body interactions, since the -potential will typically calculate energies and foces for small groups -of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to -find the additional atoms in the group. It is typically non-physical -to think of excluding an interaction between a particular pair of -atoms when the potential computes 3-body or 4-body interactions. -

    -

    However, you can still use the pair_coeff none setting or the -neigh_modify exclude command to exclude certain -type pairs from the neighbor list that will be passed to a manybody -sub-style. This will alter the calculations made by a many-body -potential, since it builds its list of 3-body, 4-body, etc -interactions from the pair list. You will need to think carefully as -to whether it produces a physically meaningful result for your model. -

    -

    For example, imagine you have two atom types in your model, type 1 for -atoms in one surface, and type 2 for atoms in the other, and you wish -to use a Tersoff potential to compute interactions within each -surface, but not between surfaces. Then either of these two command -sequences would implement that model: -

    -
    pair_style hybrid tersoff
-pair_coeff * * tersoff SiC.tersoff C C
-pair_coeff 1 2 none 
-
    -
    pair_style tersoff
-pair_coeff * * SiC.tersoff C C
-neigh_modify exclude type 1 2 
-
    -

    Either way, only neighbor lists with 1-1 or 2-2 interactions would be -passed to the Tersoff potential, which means it would compute no -3-body interactions containing both type 1 and 2 atoms. -

    -

    Here is another example, using hybrid/overlay, to use 2 many-body -potentials together, in an overlapping manner. Imagine you have CNT -(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C -interactions, and AIREBO for C/C interactions. Si atoms are type 1; C -atoms are type 2. Something like this will work: -

    -
    pair_style hybrid/overlay tersoff airebo 3.0
-pair_coeff * * tersoff SiC.tersoff.custom Si C
-pair_coeff * * airebo CH.airebo NULL C 
-
    -

    Note that to prevent the Tersoff potential from computing C/C -interactions, you would need to modify the SiC.tersoff file to turn -off C/C interaction, i.e. by setting the appropriate coefficients to -0.0. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. -

    -

    Since the hybrid and hybrid/overlay styles delegate computation -to the individual sub-styles, the suffix versions of the hybrid -and hybrid/overlay styles are used to propagate the corresponding -suffix to all sub-styles, if those versions exist. Otherwise the -non-accelerated version will be used. -

    -

    The individual accelerated sub-styles are part of the USER-CUDA, GPU, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the -Making LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    Any pair potential settings made via the -pair_modify command are passed along to all -sub-styles of the hybrid potential. -

    -

    For atom type pairs I,J and I != J, if the sub-style assigned to I,I -and J,J is the same, and if the sub-style allows for mixing, then the -coefficients for I,J can be mixed. This means you do not have to -specify a pair_coeff command for I,J since the I,J type pair will be -assigned automatically to the sub-style defined for both I,I and J,J -and its coefficients generated by the mixing rule used by that -sub-style. For the hybrid/overlay style, there is an additional -requirement that both the I,I and J,J pairs are assigned to a single -sub-style. See the "pair_modify" command for details of mixing rules. -See the See the doc page for the sub-style to see if allows for -mixing. -

    -

    The hybrid pair styles supports the pair_modify -shift, table, and tail options for an I,J pair interaction, if the -associated sub-style supports it. -

    -

    For the hybrid pair styles, the list of sub-styles and their -respective settings are written to binary restart -files, so a pair_style command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file. Thus, pair_coeff commands need to be re-specified in the -restart input script. -

    -

    These pair styles support the use of the inner, middle, and -outer keywords of the run_style respa command, if -their sub-styles do. -

    -

    Restrictions: -

    -

    When using a long-range Coulombic solver (via the -kspace_style command) with a hybrid pair_style, -one or more sub-styles will be of the "long" variety, -e.g. lj/cut/coul/long or buck/coul/long. You must insure that the -short-range Coulombic cutoff used by each of these long pair styles is -the same or else LAMMPS will generate an error. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_kim.html b/doc/doc2/pair_kim.html deleted file mode 100644 index 7ff025a96a..0000000000 --- a/doc/doc2/pair_kim.html +++ /dev/null @@ -1,123 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style kim command -

    -

    Syntax: -

    -
    pair_style kim virialmode model printflag 
-
    -
    • virialmode = KIMvirial or LAMMPSvirial -
    • model = name of KIM model (potential) -
    • printflag = 1/0 do or do not print KIM descriptor file, optional -
    -

    Examples: -

    -
    pair_style kim KIMvirial model_Ar_P_Morse
-pair_coeff * * Ar Ar 
-
    -
    pair_style kim KIMvirial model_Ar_P_Morse 1
-pair_coeff * * Ar Ar 
-
    -

    Description: -

    -

    This pair style is a wrapper on the Knowledge Base for Interatomic -Models (KIM) repository of interatomic potentials, -so that they can be used by LAMMPS scripts. -

    -

    In KIM lingo, a potential is a "model" and a model contains both the -analytic formulas that define the potential as well as the parameters -needed to run it for one or more materials, including coefficients and -cutoffs. -

    -

    The argument virialmode determines how the global virial is -calculated. If KIMvirial is specified, the KIM model performs the -global virial calculation (if it knows how). If LAMMPSvirial is -specified, LAMMPS computes the global virial using its fdotr mechanism. -

    -

    The argument model is the name of the KIM model for a specific -potential as KIM defines it. In principle, LAMMPS can invoke any KIM -model. You should get an error or warning message from either LAMMPS -or KIM if there is an incompatibility. -

    -

    The argument printflag is optional. If it is set to a non-zero -value then a KIM dsecriptor file is printed when KIM is invoked. This -can be useful for debugging. The default is to not print this file. -

    -

    Only a single pair_coeff command is used with the kim style which -specifies the mapping of LAMMPS atom types to KIM elements. This is -done by specifying N additional arguments after the * * in the -pair_coeff command, where N is the number of LAMMPS atom types: -

    -
    • N element names = mapping of KIM elements to atom types -
    -

    As an example, imagine the KIM model supports Si and C atoms. If your -LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si, -and the 4th to be C, you would use the following pair_coeff command: -

    -
    pair_coeff * * Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to Si as -defined within KIM. The final C argument maps LAMMPS atom type 4 to C -as defined within KIM. If a mapping value is specified as NULL, the -mapping is not performed. This can only be used when a kim -potential is used as part of the hybrid pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. -

    -
    - -

    In addition to the usual LAMMPS error messages, the KIM library itself -may generate errors, which should be printed to the screen. In this -case it is also useful to check the kim.log file for additional error -information. This file kim.log should be generated in the same -directory where LAMMPS is running. -

    -

    To download, build, and install the KIM library on your system, see -the lib/kim/README file. Once you have done this and built LAMMPS -with the KIM package installed you can run the example input scripts -in examples/kim. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since KIM stores the potential parameters. -Thus, you need to re-specify the pair_style and pair_coeff commands in -an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the KIM package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This current version of pair_style kim is compatible with the -kim-api package version 1.6.0 and higher. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_lcbop.html b/doc/doc2/pair_lcbop.html deleted file mode 100644 index 8b407d6729..0000000000 --- a/doc/doc2/pair_lcbop.html +++ /dev/null @@ -1,103 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lcbop command -

    -

    Syntax: -

    -
    pair_style lcbop 
-
    -

    Examples: -

    -
    pair_style lcbop
-pair_coeff * * ../potentials/C.lcbop C 
-
    -

    Description: -

    -

    The lcbop pair style computes the long-range bond-order potential -for carbon (LCBOP) of (Los and Fasolino). See section II in -that paper for the analytic equations associated with the potential. -

    -

    Only a single pair_coeff command is used with the lcbop style which -specifies an LCBOP potential file with parameters for specific -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of LCBOP elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, if your LAMMPS simulation has 4 atom types and you want -the 1st 3 to be C you would use the following pair_coeff command: -

    -
    pair_coeff * * C.lcbop C C C NULL 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first C argument maps LAMMPS atom type 1 to the C element in the -LCBOP file. If a mapping value is specified as NULL, the mapping is -not performed. This can be used when a lcbop potential is used as -part of the hybrid pair style. The NULL values are placeholders for -atom types that will be used with other potentials. -

    -

    The parameters/coefficients for the LCBOP potential as applied to C -are listed in the C.lcbop file to agree with the original (Los and -Fasolino) paper. Thus the parameters are specific to this -potential and the way it was fit, so modifying the file should be done -carefully. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair styles is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

    -

    This pair potential requires the newton setting to be -"on" for pair interactions. -

    -

    The C.lcbop potential file provided with LAMMPS (see the potentials -directory) is parameterized for metal units. You can use -the LCBOP potential with any LAMMPS units, but you would need to -create your own LCBOP potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_airebo, pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Los and Fasolino) J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107 -(2003). -

    - diff --git a/doc/doc2/pair_line_lj.html b/doc/doc2/pair_line_lj.html deleted file mode 100644 index 26b801f808..0000000000 --- a/doc/doc2/pair_line_lj.html +++ /dev/null @@ -1,142 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style line/lj command -

    -

    pair_style line/lj/omp command -

    -

    Syntax: -

    -
    pair_style line/lj cutoff 
-
    -

    cutoff = global cutoff for interactions (distance units) -

    -

    Examples: -

    -
    pair_style line/lj 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5 
-
    -

    Description: -

    -

    Style line/lj treats particles which are line segments as a set of -small spherical particles that tile the line segment length as -explained below. Interactions between two line segments, each with N1 -and N2 spherical particles, are calculated as the pairwise sum of -N1*N2 Lennard-Jones interactions. Interactions between a line segment -with N spherical particles and a point particle are treated as the -pairwise sum of N Lennard-Jones interactions. See the pair_style -lj/cut doc page for the definition of Lennard-Jones -interactions. -

    -

    The cutoff distance for an interaction between 2 line segments, or -between a line segment and a point particle, is calculated from the -position of the line segment (its center), not between pairs of -individual spheres comprising the line segment. Thus an interaction -is either calculated in its entirety or not at all. -

    -

    The set of non-overlapping spherical particles that represent a line -segment, for purposes of this pair style, are generated in the -following manner. Their size is a function of the line segment length -and the specified sigma for that particle type. If a line segment has -a length L and is of type I, then the number of spheres N that -represent the segment is calculated as N = L/sigma_II, rounded up to -an integer value. Thus if L is not evenly divisibly by sigam_II, N is -incremented to include one extra sphere. In this case, the spheres -must be slightly smaller than sigma_II so as not to overlap, so a new -sigma-prime is chosen as the sphere diameter, such that L/N = -sigma-prime. Thus the line segment interacts with other segments or -point particles as a collection of N spheres of diameter sigma-prime, -evenly spaced along the line segment, so as to exactly cover its -length. -

    -

    The LJ interaction between 2 spheres on different line segments of -types I,J is computed with an arithmetic mixing of the sigma values of -the 2 spheres and using the specified epsilon value for I,J atom -types. Note that because the sigma values for line segment spheres is -computed using only sigma_II values, specific to the line segment's -type, this means that any specified sigma_IJ values (for I != J) are -effectively ignored. -

    -

    For style line/lj, the following coefficients must be defined for -each pair of atoms types via the pair_coeff command -as in the examples above, or in the data file or restart files read by -the read_data or read_restart -commands: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global cutoff -is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of this pair style can be mixed. The -default mix value is geometric. See the "pair_modify" command for -details. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Defining particles to be line segments so they participate in -line/line or line/particle interactions requires the use the -atom_style line command. -

    -

    Related commands: -

    -

    pair_coeff, pair_style tri/lj -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_list.html b/doc/doc2/pair_list.html deleted file mode 100644 index b0981813f3..0000000000 --- a/doc/doc2/pair_list.html +++ /dev/null @@ -1,154 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style list command -

    -

    Syntax: -

    -
    pair_style list listfile cutoff keyword 
-
    -
    • listfile = name of file with list of pairwise interactions -
    • cutoff = global cutoff (distance units) -
    • keyword = optional flag nocheck or check (default is check) -
    -

    Examples: -

    -
    pair_style list restraints.txt 200.0
-pair_coeff * * 
-
    -
    pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff 3* 3* list 
-
    -

    Description: -

    -

    Style list computes interactions between explicitly listed pairs of -atoms with the option to select functional form and parameters for -each individual pair. Because the parameters are set in the list -file, the pair_coeff command has no parameters (but still needs to be -provided). The check and nocheck keywords enable/disable a test -that checks whether all listed bonds were present and computed. -

    -

    This pair style can be thought of as a hybrid between bonded, -non-bonded, and restraint interactions. It will typically be used as -an additional interaction within the hybrid/overlay pair style. It -currently supports three interaction styles: a 12-6 Lennard-Jones, a -Morse and a harmonic potential. -

    -

    The format of the list file is as follows: -

    -
    • one line per pair of atoms - -
    • empty lines will be ignored - -
    • comment text starts with a '#' character - -
    • line syntax: ID1 ID2 style coeffs cutoff - -
        ID1 = atom ID of first atom
-  ID2 = atom ID of second atom
-  style = style of interaction
-  coeffs = list of coeffs
-  cutoff = cutoff for interaction (optional) 
-
      - -
    -

    The cutoff parameter is optional. If not specified, the global cutoff -is used. -

    -

    Here is an example file: -

    -
    # this is a comment 
-
    -
    15 259 lj126     1.0 1.0      50.0
-15 603 morse    10.0 1.2 2.0  10.0 # and another comment 
-18 470 harmonic 50.0 1.2       5.0  
-
    -

    The style lj126 computes pairwise interactions with the formula -

    -
    -
    -

    and the coefficients: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    -

    The style morse computes pairwise interactions with the formula -

    -
    -
    -

    and the coefficients: -

    -
    • D0 (energy units) -
    • alpha (1/distance units) -
    • r0 (distance units) -
    -

    The style harmonic computes pairwise interactions with the formula -

    -
    -
    -

    and the coefficients: -

    -
    • K (energy units) -
    • r0 (distance units) -
    -

    Note that the usual 1/2 factor is included in K. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support mixing since all parameters are -explicit for each pair. -

    -

    The pair_modify shift option is supported by this -pair style. -

    -

    The pair_modify table and tail options are not -relevant for this pair style. -

    -

    This pair style does not write its information to binary restart -files, so pair_style and pair_coeff commands need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style does not use a neighbor list and instead identifies -atoms by their IDs. This has two consequences: 1) The cutoff has to be -chosen sufficiently large, so that the second atom of a pair has to be -a ghost atom on the same node on which the first atom is local; -otherwise the interaction will be skipped. You can use the check -option to detect, if interactions are missing. 2) Unlike other pair -styles in LAMMPS, an atom I will not interact with multiple images of -atom J (assuming the images are within the cutoff distance), but only -with the nearest image. -

    -

    This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the Making of -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, -pair_style hybrid/overlay, -pair_style lj/cut, -pair_style morse, -bond_style harmonic -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_lj.html b/doc/doc2/pair_lj.html deleted file mode 100644 index aed88ee4f6..0000000000 --- a/doc/doc2/pair_lj.html +++ /dev/null @@ -1,366 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/cut command -

    -

    pair_style lj/cut/cuda command -

    -

    pair_style lj/cut/gpu command -

    -

    pair_style lj/cut/intel command -

    -

    pair_style lj/cut/kk command -

    -

    pair_style lj/cut/opt command -

    -

    pair_style lj/cut/omp command -

    -

    pair_style lj/cut/coul/cut command -

    -

    pair_style lj/cut/coul/cut/cuda command -

    -

    pair_style lj/cut/coul/cut/gpu command -

    -

    pair_style lj/cut/coul/cut/omp command -

    -

    pair_style lj/cut/coul/debye command -

    -

    pair_style lj/cut/coul/debye/cuda command -

    -

    pair_style lj/cut/coul/debye/gpu command -

    -

    pair_style lj/cut/coul/debye/kk command -

    -

    pair_style lj/cut/coul/debye/omp command -

    -

    pair_style lj/cut/coul/dsf command -

    -

    pair_style lj/cut/coul/dsf/gpu command -

    -

    pair_style lj/cut/coul/dsf/kk command -

    -

    pair_style lj/cut/coul/dsf/omp command -

    -

    pair_style lj/cut/coul/long command -

    -

    pair_style lj/cut/coul/long/cs command -

    -

    pair_style lj/cut/coul/long/cuda command -

    -

    pair_style lj/cut/coul/long/gpu command -

    -

    pair_style lj/cut/coul/long/intel command -

    -

    pair_style lj/cut/coul/long/opt command -

    -

    pair_style lj/cut/coul/long/omp command -

    -

    pair_style lj/cut/coul/msm command -

    -

    pair_style lj/cut/coul/msm/gpu command -

    -

    pair_style lj/cut/coul/msm/omp command -

    -

    pair_style lj/cut/tip4p/cut command -

    -

    pair_style lj/cut/tip4p/cut/omp command -

    -

    pair_style lj/cut/tip4p/long command -

    -

    pair_style lj/cut/tip4p/long/omp command -

    -

    pair_style lj/cut/tip4p/long/opt command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = lj/cut or lj/cut/coul/cut or lj/cut/coul/debye or lj/cut/coul/dsf or lj/cut/coul/long or lj/cut/coul/long/cs or lj/cut/coul/msm or lj/cut/tip4p/long -
    • args = list of arguments for a particular style -
    -
      lj/cut args = cutoff
-    cutoff = global cutoff for Lennard Jones interactions (distance units)
-  lj/cut/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/debye args = kappa cutoff (cutoff2)
-    kappa = inverse of the Debye length (inverse distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/dsf args = alpha cutoff (cutoff2)
-    alpha = damping parameter (inverse distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (distance units)
-  lj/cut/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/msm args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/tip4p/cut args = otype htype btype atype qdist cutoff (cutoff2)
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/tip4p/long args = otype htype btype atype qdist cutoff (cutoff2)
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
    -

    Examples: -

    -
    pair_style lj/cut 2.5
-pair_coeff * * 1 1
-pair_coeff 1 1 1 1.1 2.8 
-
    -
    pair_style lj/cut/coul/cut 10.0
-pair_style lj/cut/coul/cut 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-pair_coeff 1 1 100.0 3.5 9.0 9.0 
-
    -
    pair_style lj/cut/coul/debye 1.5 3.0
-pair_style lj/cut/coul/debye 1.5 2.5 5.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5
-pair_coeff 1 1 1.0 1.5 2.5 5.0 
-
    -
    pair_style lj/cut/coul/dsf 0.05 2.5 10.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.0 2.5 
-
    -
    pair_style lj/cut/coul/long 10.0
-pair_style lj/cut/coul/long/cs 10.0
-pair_style lj/cut/coul/long 10.0 8.0
-pair_style lj/cut/coul/long/cs 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0 
-
    -
    pair_style lj/cut/coul/msm 10.0
-pair_style lj/cut/coul/msm 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0 
-
    -
    pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
-pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0 
-
    -
    pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
-pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0 
-
    -

    Description: -

    -

    The lj/cut styles compute the standard 12/6 Lennard-Jones potential, -given by -

    -
    -
    -

    Rc is the cutoff. -

    -

    Style lj/cut/coul/cut adds a Coulombic pairwise interaction given by -

    -
    -
    -

    where C is an energy-conversion constant, Qi and Qj are the charges on -the 2 atoms, and epsilon is the dielectric constant which can be set -by the dielectric command. If one cutoff is -specified in the pair_style command, it is used for both the LJ and -Coulombic terms. If two cutoffs are specified, they are used as -cutoffs for the LJ and Coulombic terms respectively. -

    -

    Style lj/cut/coul/debye adds an additional exp() damping factor -to the Coulombic term, given by -

    -
    -
    -

    where kappa is the inverse of the Debye length. This potential is -another way to mimic the screening effect of a polar solvent. -

    -

    Style lj/cut/coul/dsf computes the Coulombic term via the damped -shifted force model described in Fennell, given by: -

    -
    -
    -

    where alpha is the damping parameter and erfc() is the complementary -error-function. This potential is essentially a short-range, -spherically-truncated, charge-neutralized, shifted, pairwise 1/r -summation. The potential is based on Wolf summation, proposed as an -alternative to Ewald summation for condensed phase systems where -charge screening causes electrostatic interactions to become -effectively short-ranged. In order for the electrostatic sum to be -absolutely convergent, charge neutralization within the cutoff radius -is enforced by shifting the potential through placement of image -charges on the cutoff sphere. Convergence can often be improved by -setting alpha to a small non-zero value. -

    -

    Styles lj/cut/coul/long and lj/cut/coul/msm compute the same -Coulombic interactions as style lj/cut/coul/cut except that an -additional damping factor is applied to the Coulombic term so it can -be used in conjunction with the kspace_style -command and its ewald or pppm option. The Coulombic cutoff -specified for this style means that pairwise interactions within this -distance are computed directly; interactions outside that distance are -computed in reciprocal space. -

    -

    Style lj/cut/coul/long/cs is identical to lj/cut/coul/long except -that a term is added for the core/shell -model to allow charges on core and shell -particles to be separated by r = 0.0. -

    -

    Styles lj/cut/tip4p/cut and lj/cut/tip4p/long implement the TIP4P -water model of (Jorgensen), which introduces a massless -site located a short distance away from the oxygen atom along the -bisector of the HOH angle. The atomic types of the oxygen and -hydrogen atoms, the bond and angle types for OH and HOH interactions, -and the distance to the massless charge site are specified as -pair_style arguments. Style lj/cut/tip4p/cut uses a cutoff for -Coulomb interactions; style lj/cut/tip4p/long is for use with a -long-range Coulombic solver (Ewald or PPPM). -

    -

    IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom -IDs for the O and 2 H atoms must be consecutive, with the O atom -first. This is to enable LAMMPS to "find" the 2 H atoms associated -with each O atom. For example, if the atom ID of an O atom in a TIP4P -water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -

    -

    See the howto section for more -information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighobr list cutoff for Coulomb -interactions is effectively extended by a distance 2*qdist when using -the TIP4P pair style, to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*qdist, to shrink the size of the neighbor list. This leads -to slightly larger cost for the long-range calculation, so you can -test the trade-off for your model. -

    -

    For all of the lj/cut pair styles, the following coefficients must -be defined for each pair of atoms types via the -pair_coeff command as in the examples above, or in -the data file or restart files read by the read_data -or read_restart commands, or by mixing as -described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff1 (distance units) -
    • cutoff2 (distance units) -
    -

    Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. -

    -

    The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style lj/cut, since it -has no Coulombic terms. -

    -

    For lj/cut/coul/long and lj/cut/coul/msm and lj/cut/tip4p/cut -and lj/cut/tip4p/long only the LJ cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is geometric. See the "pair_modify" command -for details. -

    -

    All of the lj/cut pair styles support the -pair_modify shift option for the energy of the -Lennard-Jones portion of the pair interaction. -

    -

    The lj/cut/coul/long and lj/cut/tip4p/long pair styles support the -pair_modify table option since they can tabulate -the short-range portion of the long-range Coulombic interaction. -

    -

    All of the lj/cut pair styles support the -pair_modify tail option for adding a long-range -tail correction to the energy and pressure for the Lennard-Jones -portion of the pair interaction. -

    -

    All of the lj/cut pair styles write their information to binary -restart files, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. -

    -

    The lj/cut and lj/cut/coul/long pair styles support the use of the -inner, middle, and outer keywords of the run_style -respa command, meaning the pairwise forces can be -partitioned by distance at different levels of the rRESPA hierarchy. -The other styles only support the pair keyword of run_style respa. -See the run_style command for details. -

    -
    - -

    Restrictions: -

    -

    The lj/cut/coul/long and lj/cut/tip4p/long styles are part of the -KSPACE package. The lj/cut/tip4p/cut style is part of the MOLECULE -package. These styles are only enabled if LAMMPS was built with those -packages. See the Making LAMMPS section -for more info. Note that the KSPACE and MOLECULE packages are -installed by default. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Jorgensen) Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). -

    - - -

    (Fennell) C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, -234104 (2006). -

    - diff --git a/doc/doc2/pair_lj96.html b/doc/doc2/pair_lj96.html deleted file mode 100644 index 768c8fc3fd..0000000000 --- a/doc/doc2/pair_lj96.html +++ /dev/null @@ -1,116 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj96/cut command -

    -

    pair_style lj96/cut/cuda command -

    -

    pair_style lj96/cut/gpu command -

    -

    pair_style lj96/cut/omp command -

    -

    Syntax: -

    -
    pair_style lj96/cut cutoff 
-
    -
    • cutoff = global cutoff for lj96/cut interactions (distance units) -
    -

    Examples: -

    -
    pair_style lj96/cut 2.5
-pair_coeff * * 1.0 1.0 4.0
-pair_coeff 1 1 1.0 1.0 
-
    -

    Description: -

    -

    The lj96/cut style compute a 9/6 Lennard-Jones potential, instead -of the standard 12/6 potential, given by -

    -
    -
    -

    Rc is the cutoff. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global LJ -cutoff specified in the pair_style command is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is geometric. See the "pair_modify" command -for details. -

    -

    This pair style supports the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style supports the pair_modify tail -option for adding a long-range tail correction to the energy and -pressure of the pair interaction. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style supports the use of the inner, middle, and outer -keywords of the run_style respa command, meaning the -pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the run_style command for -details. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_lj_cubic.html b/doc/doc2/pair_lj_cubic.html deleted file mode 100644 index 6e450e0c20..0000000000 --- a/doc/doc2/pair_lj_cubic.html +++ /dev/null @@ -1,138 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/cubic command -

    -

    pair_style lj/cubic/gpu command -

    -

    pair_style lj/cubic/omp command -

    -

    Syntax: -

    -
    pair_style lj/cubic 
-
    -

    Examples: -

    -
    pair_style lj/cubic
-pair_coeff * * 1.0 0.8908987 
-
    -

    Description: -

    -

    The lj/cubic style computes a truncated LJ interaction potential -whose energy and force are continuous everywhere. Inside the -inflection point the interaction is identical to the standard 12/6 -Lennard-Jones potential. The LJ function outside the -inflection point is replaced with a cubic function of distance. The -energy, force, and second derivative are continuous at the inflection -point. The cubic coefficient A3 is chosen so that both energy and -force go to zero at the cutoff distance. Outside the cutoff distance -the energy and force are zero. -

    -
    -
    -

    The location of the inflection point rs is defined -by the LJ diameter, rs/sigma = (26/7)^1/6. The cutoff distance -is defined by rc/rs = 67/48 or rc/sigma = 1.737.... -The analytic expression for the -the cubic coefficient -A3*rmin^3/epsilon = 27.93... is given in the paper by -Holian and Ravelo (Holian). -

    -

    This potential is commonly used to study the shock mechanics of FCC -solids, as in Ravelo et al. (Ravelo). -

    -

    The following coefficients must be defined for each pair of atom types -via the pair_coeff command as in the example above, -or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    -

    Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum, which is -located at rmin = 2^(1/6)*sigma. In the above example, sigma = -0.8908987, so rmin = 1. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is geometric. See the "pair_modify" command -for details. -

    -

    The lj/cubic pair style does not support the -pair_modify shift option, -since pair interaction is already smoothed to 0.0 at the -cutoff. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    The lj/cubic pair style does not support the -pair_modify tail option for adding long-range tail -corrections to energy and pressure, since there are no corrections for -a potential that goes to 0.0 at the cutoff. -

    -

    The lj/cubic pair style writes its information to binary -restart files, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. -

    -

    The lj/cubic pair style can only be used via the pair -keyword of the run_style respa command. It does not -support the inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -(Holian) Holian and Ravelo, Phys Rev B, 51, 11275 (1995). - - -

    (Ravelo) Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). -

    - diff --git a/doc/doc2/pair_lj_cut_smooth.html b/doc/doc2/pair_lj_cut_smooth.html deleted file mode 100644 index 1430313a80..0000000000 --- a/doc/doc2/pair_lj_cut_smooth.html +++ /dev/null @@ -1,111 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/cut/smooth command -

    -

    pair_style lj/cut/smooth/cuda command -

    -

    pair_style lj/cut/smooth/omp command -

    -

    Syntax: -

    -
    pair_style lj/cut/smooth Rc 
-
    -
    • Rc = cutoff for lj/cut/smooth interactions (distance units) -
    -

    Examples: -

    -
    pair_style lj/cut/smooth 5.456108274435118
-pair_coeff * * 0.7242785984051078 2.598146797350056
-pair_coeff 1 1 20.0 1.3 9.0 
-
    -

    Description: -

    -

    Style lj/cut/smooth computes a LJ interaction that combines the standard -12/6 Lennard-Jones function and subtracts a linear term that includes a -cutoff distance Rc. -

    -
    -
    -

    At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff (distance units) -
    -

    If not specified, the global value for Rc is used. -

    -
    - -

    Styles with a cuda, gpu, omp, or opt suffix are functionally -the same as the corresponding style without the suffix. They have -been optimized to run faster, depending on your available hardware, as -discussed in Section_accelerate of the -manual. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT -packages, respectively. They are only enabled if LAMMPS was built with -those packages. See the Making LAMMPS -section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients and -cutoff distance can be mixed. The default mix value is geometric. -See the "pair_modify" command for details. -

    -

    This pair style does not support the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_lj_expand.html b/doc/doc2/pair_lj_expand.html deleted file mode 100644 index 4dc314a37e..0000000000 --- a/doc/doc2/pair_lj_expand.html +++ /dev/null @@ -1,120 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/expand command -

    -

    pair_style lj/expand/cuda command -

    -

    pair_style lj/expand/gpu command -

    -

    pair_style lj/expand/omp command -

    -

    Syntax: -

    -
    pair_style lj/expand cutoff 
-
    -
    • cutoff = global cutoff for lj/expand interactions (distance units) -
    -

    Examples: -

    -
    pair_style lj/expand 2.5
-pair_coeff * * 1.0 1.0 0.5
-pair_coeff 1 1 1.0 1.0 -0.2 2.0 
-
    -

    Description: -

    -

    Style lj/expand computes a LJ interaction with a distance shifted by -delta which can be useful when particles are of different sizes, since -it is different that using different sigma values in a standard LJ -formula: -

    -
    -
    -

    Rc is the cutoff which does not include the delta distance. I.e. the -actual force cutoff is the sum of cutoff + delta. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • delta (distance units) -
    • cutoff (distance units) -
    -

    The delta values can be positive or negative. The last coefficient is -optional. If not specified, the global LJ cutoff is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon, sigma, and shift -coefficients and cutoff distance for this pair style can be mixed. -Shift is always mixed via an arithmetic rule. The other -coefficients are mixed according to the pair_modify mix value. The -default mix value is geometric. See the "pair_modify" command for -details. -

    -

    This pair style supports the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style supports the pair_modify tail -option for adding a long-range tail correction to the energy and -pressure of the pair interaction. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_lj_long.html b/doc/doc2/pair_lj_long.html deleted file mode 100644 index 5b7455771b..0000000000 --- a/doc/doc2/pair_lj_long.html +++ /dev/null @@ -1,235 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/long/coul/long command -

    -

    pair_style lj/long/coul/long/omp command -

    -

    pair_style lj/long/coul/long/opt command -

    -

    pair_style lj/long/tip4p/long command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = lj/long/coul/long or lj/long/tip4p/long -
    • args = list of arguments for a particular style -
    -
      lj/long/coul/long args = flag_lj flag_coul cutoff (cutoff2)
-    flag_lj = long or cut or off
-      long = use Kspace long-range summation for dispersion 1/r^6 term
-      cut = use a cutoff on dispersion 1/r^6 term
-      off = omit disperion 1/r^6 term entirely
-    flag_coul = long or off
-      long = use Kspace long-range summation for Coulombic 1/r term
-      off = omit Coulombic term
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/long/tip4p/long args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
-    flag_lj = long or cut
-      long = use Kspace long-range summation for dispersion 1/r^6 term
-      cut = use a cutoff
-    flag_coul = long or off
-      long = use Kspace long-range summation for Coulombic 1/r term
-      off = omit Coulombic term
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
    -

    Examples: -

    -
    pair_style lj/long/coul/long cut off 2.5
-pair_style lj/long/coul/long cut long 2.5 4.0
-pair_style lj/long/coul/long long long 2.5 4.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 3 4 
-
    -
    pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
-pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0 
-
    -

    Description: -

    -

    Style lj/long/coul/long computes the standard 12/6 Lennard-Jones and -Coulombic potentials, given by -

    -
    -
    -
    -
    -

    where C is an energy-conversion constant, Qi and Qj are the charges on -the 2 atoms, epsilon is the dielectric constant which can be set by -the dielectric command, and Rc is the cutoff. If -one cutoff is specified in the pair_style command, it is used for both -the LJ and Coulombic terms. If two cutoffs are specified, they are -used as cutoffs for the LJ and Coulombic terms respectively. -

    -

    The purpose of this pair style is to capture long-range interactions -resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r -interactions. This is done by use of the flag_lj and flag_coul -settings. The In 't Veld paper has more details on when it is -appropriate to include long-range 1/r^6 interactions, using this -potential. -

    -

    Style lj/long/tip4p/long implements the TIP4P water model of -(Jorgensen), which introduces a massless site located a -short distance away from the oxygen atom along the bisector of the HOH -angle. The atomic types of the oxygen and hydrogen atoms, the bond -and angle types for OH and HOH interactions, and the distance to the -massless charge site are specified as pair_style arguments. -

    -

    IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom -IDs for the O and 2 H atoms must be consecutive, with the O atom -first. This is to enable LAMMPS to "find" the 2 H atoms associated -with each O atom. For example, if the atom ID of an O atom in a TIP4P -water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -

    -

    See the howto section for more -information on how to use the TIP4P pair style. Note that the -neighobr list cutoff for Coulomb interactions is effectively extended -by a distance 2*qdist when using the TIP4P pair style, to account for -the offset distance of the fictitious charges on O atoms in water -molecules. Thus it is typically best in an efficiency sense to use a -LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the -neighbor list. This leads to slightly larger cost for the long-range -calculation, so you can test the trade-off for your model. -

    -

    If flag_lj is set to long, no cutoff is used on the LJ 1/r^6 -dispersion term. The long-range portion can be calculated by using -the kspace_style ewald/disp or pppm/disp commands. -The specified LJ cutoff then determines which portion of the LJ -interactions are computed directly by the pair potential versus which -part is computed in reciprocal space via the Kspace style. If -flag_lj is set to cut, the LJ interactions are simply cutoff, as -with pair_style lj/cut. -

    -

    If flag_coul is set to long, no cutoff is used on the Coulombic -interactions. The long-range portion can calculated by using any of -several kspace_style command options such as -pppm or ewald. Note that if flag_lj is also set to long, then -the ewald/disp or pppm/disp Kspace style needs to be used to -perform the long-range calculations for both the LJ and Coulombic -interactions. If flag_coul is set to off, Coulombic interactions -are not computed. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff1 (distance units) -
    • cutoff2 (distance units) -
    -

    Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. -

    -

    The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. -

    -

    Note that if you are using flag_lj set to long, you -cannot specify a LJ cutoff for an atom type pair, since only one -global LJ cutoff is allowed. Similarly, if you are using flag_coul -set to long, you cannot specify a Coulombic cutoff for an atom type -pair, since only one global Coulombic cutoff is allowed. -

    -

    For lj/long/tip4p/long only the LJ cutoff can be specified -since a Coulombic cutoff cannot be specified for an individual I,J -type pair. All type pairs use the same global Coulombic cutoff -specified in the pair_style command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/long pair styles can be mixed. -The default mix value is geometric. See the "pair_modify" command -for details. -

    -

    These pair styles support the pair_modify shift -option for the energy of the Lennard-Jones portion of the pair -interaction, assuming flag_lj is cut. -

    -

    These pair styles support the pair_modify table and -table/disp options since they can tabulate the short-range portion of -the long-range Coulombic and dispersion interactions. -

    -

    Thes pair styles do not support the pair_modify -tail option for adding a long-range tail correction to the -Lennard-Jones portion of the energy and pressure. -

    -

    These pair styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    The pair lj/long/coul/long styles support the use of the inner, -middle, and outer keywords of the run_style respa -command, meaning the pairwise forces can be partitioned by distance at -different levels of the rRESPA hierarchy. See the -run_style command for details. -

    -
    - -

    Restrictions: -

    -

    These styles are part of the KSPACE package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. Note that -the KSPACE package is installed by default. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (In 't Veld) In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007). -

    - diff --git a/doc/doc2/pair_lj_sf.html b/doc/doc2/pair_lj_sf.html deleted file mode 100644 index 582c4604e8..0000000000 --- a/doc/doc2/pair_lj_sf.html +++ /dev/null @@ -1,121 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/sf command -

    -

    pair_style lj/sf/omp command -

    -

    Syntax: -

    -
    pair_style lj/sf cutoff 
-
    -
    • cutoff = global cutoff for Lennard-Jones interactions (distance units) -
    -

    Examples: -

    -
    pair_style lj/sf 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.0 3.0 
-
    -

    Description: -

    -

    Style lj/sf computes a truncated and force-shifted LJ interaction -(Shifted Force Lennard-Jones), so that both the potential and the -force go continuously to zero at the cutoff (Toxvaerd): -

    -
    -
    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global -LJ cutoff specified in the pair_style command is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma -coefficients and cutoff distance for this pair style can be mixed. -Rin is a cutoff value and is mixed like the cutoff. The -default mix value is geometric. See the "pair_modify" command for -details. -

    -

    The pair_modify shift option is not relevant for -this pair style, since the pair interaction goes to 0.0 at the cutoff. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Toxvaerd) Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011). -

    - diff --git a/doc/doc2/pair_lj_smooth.html b/doc/doc2/pair_lj_smooth.html deleted file mode 100644 index f5d381fe3f..0000000000 --- a/doc/doc2/pair_lj_smooth.html +++ /dev/null @@ -1,130 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/smooth command -

    -

    pair_style lj/smooth/cuda command -

    -

    pair_style lj/smooth/omp command -

    -

    Syntax: -

    -
    pair_style lj/smooth Rin Rc 
-
    -
    • Rin = inner cutoff beyond which force smoothing will be applied (distance units) -
    • Rc = outer cutoff for lj/smooth interactions (distance units) -
    -

    Examples: -

    -
    pair_style lj/smooth 8.0 10.0
-pair_coeff * * 10.0 1.5
-pair_coeff 1 1 20.0 1.3 7.0 9.0 
-
    -

    Description: -

    -

    Style lj/smooth computes a LJ interaction with a force smoothing -applied between the inner and outer cutoff. -

    -
    -
    -

    The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to -cause the force to vary smoothly from the inner cutoff Rin to the -outer cutoff Rc. -

    -

    At the inner cutoff the force and its 1st derivative -will match the unsmoothed LJ formula. At the outer cutoff the force -and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0. -

    -

    IMPORTANT NOTE: this force smoothing causes the energy to be -discontinuous both in its values and 1st derivative. This can lead to -poor energy conservation and may require the use of a thermostat. -Plot the energy and force resulting from this formula via the -pair_write command to see the effect. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • innner (distance units) -
    • outer (distance units) -
    -

    The last 2 coefficients are optional inner and outer cutoffs. If not -specified, the global values for Rin and Rc are used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon, sigma, Rin -coefficients and the cutoff distance for this pair style can be mixed. -Rin is a cutoff value and is mixed like the cutoff. The other -coefficients are mixed according to the pair_modify mix option. The -default mix value is geometric. See the "pair_modify" command for -details. -

    -

    This pair style supports the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff, pair -lj/smooth/linear -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_lj_smooth_linear.html b/doc/doc2/pair_lj_smooth_linear.html deleted file mode 100644 index 43f35bbba1..0000000000 --- a/doc/doc2/pair_lj_smooth_linear.html +++ /dev/null @@ -1,111 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/smooth/linear command -

    -

    pair_style lj/smooth/linear/omp command -

    -

    Syntax: -

    -
    pair_style lj/smooth/linear Rc 
-
    -
    • Rc = cutoff for lj/smooth/linear interactions (distance units) -
    -

    Examples: -

    -
    pair_style lj/smooth/linear 5.456108274435118
-pair_coeff * * 0.7242785984051078 2.598146797350056
-pair_coeff 1 1 20.0 1.3 9.0 
-
    -

    Description: -

    -

    Style lj/smooth/linear computes a LJ interaction that combines the -standard 12/6 Lennard-Jones function and subtracts a linear term that -includes the cutoff distance Rc, as in this formula: -

    -
    -
    -

    At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global value -for Rc is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance can be mixed. The default mix value is geometric. -See the "pair_modify" command for details. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant for -this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff, pair lj/smooth -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_lj_soft.html b/doc/doc2/pair_lj_soft.html deleted file mode 100644 index 9b49d3a3ab..0000000000 --- a/doc/doc2/pair_lj_soft.html +++ /dev/null @@ -1,299 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/cut/soft command -

    -

    pair_style lj/cut/soft/omp command -

    -

    pair_style lj/cut/coul/cut/soft command -

    -

    pair_style lj/cut/coul/cut/soft/omp command -

    -

    pair_style lj/cut/coul/long/soft command -

    -

    pair_style lj/cut/coul/long/soft/omp command -

    -

    pair_style lj/cut/tip4p/long/soft command -

    -

    pair_style lj/cut/tip4p/long/soft/omp command -

    -

    pair_style lj/charmm/coul/long/soft command -

    -

    pair_style lj/charmm/coul/long/soft/omp command -

    -

    pair_style coul/cut/soft command -

    -

    pair_style coul/cut/soft/omp command -

    -

    pair_style coul/long/soft command -

    -

    pair_style coul/long/soft/omp command -

    -

    pair_style tip4p/long/soft command -

    -

    pair_style tip4p/long/soft/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = lj/cut/soft or lj/cut/coul/cut/soft or lj/cut/coul/long/soft or lj/cut/tip4p/long/soft or lj/charmm/coul/long/soft or coul/cut/soft or coul/long/soft or tip4p/long/soft -
    • args = list of arguments for a particular style -
    -
      lj/cut/soft args = n alpha_lj cutoff
-    n, alpha_LJ = parameters of soft-core potential
-    cutoff = global cutoff for Lennard-Jones interactions (distance units)
-  lj/cut/coul/cut/soft args = n alpha_LJ alpha_C cutoff (cutoff2)
-    n, alpha_LJ, alpha_C = parameters of soft-core potential
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/long/soft args = n alpha_LJ alpha_C cutoff
-    n, alpha_LJ, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/tip4p/long/soft args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    n, alpha_LJ, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/charmm/coul/long/soft args = n alpha_LJ alpha_C inner outer (cutoff)
-    n, alpha_LJ, alpha_C = parameters of the soft-core potential
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
-    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
-  coul/cut/soft args = n alpha_C cutoff
-    n, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for Coulomb interactions (distance units)
-  coul/long/soft args = n alpha_C cutoff
-    n, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for Coulomb interactions (distance units)
-  tip4p/long/soft args = otype htype btype atype qdist n alpha_C cutoff
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    n, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for Coulomb interactions (distance units)
-
-
    -

    Examples: -

    -
    pair_style lj/cut/soft 2.0 0.5 9.5
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 1.0 9.5 
-
    -
    pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
-pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 0.5 10.0
-pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 
-
    -
    pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
-pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 0.0 10.0
-pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 
-
    -
    pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
-pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
-pair_coeff * * 0.155 3.1536 1.0
-pair_coeff 1 1 0.155 3.1536 1.0 9.5 
-
    -
    pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
-pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 
-
    -
    pair_style coul/long/soft 1.0 10.0 9.5
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0 9.5 
-
    -
    pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0 9.5 
-
    -

    Description: -

    -

    The lj/cut/soft style and substyles compute the 12/6 Lennard-Jones -and Coulomb potential modified by a soft core, in order to avoid -singularities during free energy calculations when sites are created -or anihilated (Beutler), -

    -
    -
    -

    Coulomb interactions are also damped with a soft core at short -distance, -

    -
    -
    -

    In the Coulomb part C is an energy-conversion constant, q_i and q_j -are the charges on the 2 atoms, and epsilon is the dielectric constant -which can be set by the dielectric command. -

    -

    The coefficient lambda is an activation parameter. When lambda = 1 the -pair potentiel is identical to a Lennard-Jones term or a Coulomb term -or a combination of both. When lambda = 0 the interactions are -deactivated. The transition between these two extrema is smoothed by a -soft repulsive core in order to avoid singularities in potential -energy and forces when sites are created or anihilated and can overlap -(Beutler). -

    -

    The paratemers n, alpha_LJ and alpha_C are set in the -pair_style command, before the cutoffs. Usual -choices for the exponent are n = 2 or n = 1. For the remaining -coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are -appropriate choices. Plots of the LJ and Coulomb terms are shown -below, for lambda ranging from 1 to 0 every 0.1. -

    -
    -
    -

    For the lj/cut/coul/cut/soft or lj/cut/coul/long/soft pair styles, -the following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • lambda (activation parameter between 0 and 1) -
    • cutoff1 (distance units) -
    • cutoff2 (distance units) -
    -

    The latter two coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style lj/cut/soft, -since it has no Coulombic terms. For the coul/cut/soft and -coul/long/soft only lambda and the optional cutoff2 are to be -specified. -

    -

    Style lj/cut/tip4p/long/soft implements a soft-core version of the -TIP4P water model. The usage of this pair style is documented in the -pair_lj styles. The soft-core version introduces the -lambda parameter to the list of arguments, after epsilon and sigma in -the pair_coeff command. The paratemers n, alpha_LJ -and alpha_C are set in the pair_style command, -before the cutoffs. -

    -

    Style lj/charmm/coul/long/soft implements a soft-core version of the -CHARMM version of LJ interactions with an additional switching -function S(r) that ramps the energy and force smoothly to zero between -an inner and outer cutoff. The usage of this pair style is documented -in the pair_charmm styles. The soft-core version -introduces the lambda parameter to the list of arguments, after -epsilon and sigma in the pair_coeff command (and -before the optional eps14 and sigma14). The paratemers n, -alpha_LJ and alpha_C are set in the pair_style -command, before the cutoffs. -

    -

    The coul/cut/soft, coul/long/soft and tip4p/long/soft substyles -are designed to be combined with other pair potentials via the -pair_style hybrid/overlay command. This is because -they have no repulsive core. Hence, if used by themselves, there will -be no repulsion to keep two oppositely charged particles from -overlapping each other. In this case, if lambda = 1, a singularity may -occur. These substyles are suitable to represent charges embedded in -the Lennard-Jones radius of another site (for example hydrogen atoms -in several water models). -

    -

    IMPORTANT NOTES: When using the core-softed Coulomb potentials with -long-range solvers (coul/long/soft, lj/cut/coul/long/soft, etc.) -in a free energy calculation in which sites holding electrostatic -charges are being created or anihilated (using -fix_adapt/fep and compute_fep) -it is important to adapt both the lambda activation parameter (from 0 -to 1, or the reverse) and the value of the charge (from 0 to its final -value, or the reverse). This ensures that long-range electrostatic -terms (kspace) are correct. It is not necessary to use core-softed -Coulomb potentials if the van der Waals site is present during the -free-energy route, thus avoiding overlap of the charges. Examples are -provided in the LAMMPS source directory tree, under examples/USER/fep. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, tail correction, restart info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for this pair style can be mixed. -The default mix value is geometric. See the "pair_modify" command -for details. -

    -

    These pair styles support the pair_modify shift -option for the energy of the Lennard-Jones portion of the pair -interaction. -

    -

    These pair styles support the pair_modify tail -option for adding a long-range tail correction to the energy and -pressure for the Lennard-Jones portion of the pair interaction. -

    -

    These pair styles write information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -
    - -

    Restrictions: -

    -

    To avoid division by zero do not set sigma = 0; use the lambda -parameter instead to activate/deactivate interactions, or use -epsilon = 0 and sigma = 1. Alternatively, when sites do not -interact though the Lennard-Jones term the coul/long/soft or -similar substyle can be used via the -pair_style hybrid/overlay command. -

    -
    - -

    All of the plain soft pair styles are part of the USER-FEP package. -The long styles also requires the KSPACE package to be installed. -They are only enabled if LAMMPS was built with those packages. See -the Making LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, fix_adapt, -fix_adapt/fep, compute_fep -

    -

    Default: none -

    -
    - - - -

    (Beutler) Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem -Phys Lett, 222, 529 (1994). -

    - diff --git a/doc/doc2/pair_lubricate.html b/doc/doc2/pair_lubricate.html deleted file mode 100644 index cdef2a104f..0000000000 --- a/doc/doc2/pair_lubricate.html +++ /dev/null @@ -1,239 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lubricate command -

    -

    pair_style lubricate/omp command -

    -

    pair_style lubricate/poly command -

    -

    pair_style lubricate/poly/omp command -

    -

    Syntax: -

    -
    pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF 
-
    -
    • style = lubricate or lubricate/poly -
    • mu = dynamic viscosity (dynamic viscosity units) -
    • flaglog = 0/1 to exclude/include log terms in the lubrication approximation -
    • flagfld = 0/1 to exclude/include Fast Lubrication Dynamics (FLD) effects -
    • cutinner = inner cutoff distance (distance units) -
    • cutoff = outer cutoff for interactions (distance units) -
    • flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions -
    • flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms -
    -

    Examples: (all assume radius = 1) -

    -
    pair_style lubricate 1.5 1 1 2.01 2.5
-pair_coeff 1 1 2.05 2.8
-pair_coeff * * 
-
    -
    pair_style lubricate 1.5 1 1 2.01 2.5
-pair_coeff * *
-variable mu equal ramp(1,2)
-fix 1 all adapt 1 pair lubricate mu * * v_mu 
-
    -

    Description: -

    -

    Styles lubricate and lubricate/poly compute hydrodynamic -interactions between mono-disperse spherical particles in a pairwise -fashion. The interactions have 2 components. The first is -Ball-Melrose lubrication terms via the formulas in (Ball and -Melrose) -

    -
    -
    -

    which represents the dissipation W between two nearby particles due to -their relative velocities in the presence of a background solvent with -viscosity mu. Note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. -

    -

    The Asq (squeeze) term is the strongest and is included if flagHI is -set to 1 (default). It scales as 1/gap where gap is the separation -between the surfaces of the 2 particles. The Ash (shear) and Apu -(pump) terms are only included if flaglog is set to 1. They are the -next strongest interactions, and the only other singular interaction, -and scale as log(gap). Note that flaglog = 1 and flagHI = 0 is -invalid, and will result in a warning message, after which flagHI will -be set to 1. The Atw (twist) term is currently not included. It is -typically a very small contribution to the lubrication forces. -

    -

    The flagHI and flagVF settings are optional. Neither should be -used, or both must be defined. -

    -

    Cutinner sets the minimum center-to-center separation that will be -used in calculations irrespective of the actual separation. Cutoff -is the maximum center-to-center separation at which an interaction is -computed. Using a cutoff less than 3 radii is recommended if -flaglog is set to 1. -

    -

    The other component is due to the Fast Lubrication Dynamics (FLD) -approximation, described in (Kumar), which can be -represented by the following equation -

    -
    -
    -

    where U represents the velocities and angular velocities of the -particles, U^infty represents the velocity and the angular velocity -of the undisturbed fluid, and E^infty represents the rate of strain -tensor of the undisturbed fluid with viscosity mu. Again, note that -this is dynamic viscosity which has units of mass/distance/time, not -kinematic viscosity. Volume fraction corrections to R_FU are included -as long as flagVF is set to 1 (default). -

    -

    IMPORTANT NOTE: When using the FLD terms, these pair styles are -designed to be used with explicit time integration and a -correspondingly small timestep. Thus either fix -nve/sphere or fix -nve/asphere should be used for time integration. -To perform implicit FLD, see the pair_style -lubricateU command. -

    -

    Style lubricate requires monodisperse spherical particles; style -lubricate/poly allows for polydisperse spherical particles. -

    -

    The viscosity mu can be varied in a time-dependent manner over the -course of a simluation, in which case in which case the pair_style -setting for mu will be overridden. See the fix adapt -command for details. -

    -

    If the suspension is sheared via the fix deform -command then the pair style uses the shear rate to adjust the -hydrodynamic interactions accordingly. Volume changes due to fix -deform are accounted for when computing the volume fraction -corrections to R_FU. -

    -

    When computing the volume fraction corrections to R_FU, the presence -of walls (whether moving or stationary) will affect the volume -fraction available to colloidal particles. This is currently accounted -for with the following types of walls: wall/lj93, -wall/lj126, wall/colloid, and -wall/harmonic. For these wall styles, the correct -volume fraction will be used when walls do not coincide with the box -boundary, as well as when walls move and thereby cause a change in the -volume fraction. Other wall styles will still work, but they will -result in the volume fraction being computed based on the box -boundaries. -

    -

    Since lubrication forces are dissipative, it is usually desirable to -thermostat the system at a constant temperature. If Brownian motion -(at a constant temperature) is desired, it can be set using the -pair_style brownian command. These pair styles -and the brownian style should use consistent parameters for mu, -flaglog, flagfld, cutinner, cutoff, flagHI and flagVF. -

    -
    - -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • cutinner (distance units) -
    • cutoff (distance units) -
    -

    The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in this section of -the manual. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See this section of the manual for more -instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is geometric. See -the "pair_modify" command for details. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Only spherical monodisperse particles are allowed for pair_style -lubricate. -

    -

    Only spherical particles are allowed for pair_style lubricate/poly. -

    -

    These pair styles will not restart exactly when using the -read_restart command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -read_restart command for more details. -

    -

    Related commands: -

    -

    pair_coeff, pair_style -lubricateU -

    -

    Default: -

    -

    The default settings for the optional args are flagHI = 1 and flagVF = -1. -

    -
    - - - -

    (Ball) Ball and Melrose, Physica A, 247, 444-472 (1997). -

    - - -

    (Kumar) Kumar and Higdon, Phys Rev E, 82, 051401 (2010). See also -his thesis for more details: A. Kumar, "Microscale Dynamics in -Suspensions of Non-spherical Particles", Thesis, University of -Illinois Urbana-Champaign, -(2010). (https://www.ideals.illinois.edu/handle/2142/16032) -

    - diff --git a/doc/doc2/pair_lubricateU.html b/doc/doc2/pair_lubricateU.html deleted file mode 100644 index 42a596c70b..0000000000 --- a/doc/doc2/pair_lubricateU.html +++ /dev/null @@ -1,225 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lubricateU command -

    -

    pair_style lubricateU/poly command -

    -

    Syntax: -

    -
    pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF 
-
    -
    • style = lubricateU or lubricateU/poly -
    • mu = dynamic viscosity (dynamic viscosity units) -
    • flaglog = 0/1 to exclude/include log terms in the lubrication approximation -
    • cutinner = inner cut off distance (distance units) -
    • cutoff = outer cutoff for interactions (distance units) -
    • gdot = shear rate (1/time units) -
    • flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions -
    • flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms -
    -

    Examples: (all assume radius = 1) -

    -
    pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
-pair_coeff 1 1 2.05 2.8
-pair_coeff * * 
-
    -

    Description: -

    -

    Styles lubricateU and lubricateU/poly compute velocities and -angular velocities such that the hydrodynamic interaction balances the -force and torque due to all other types of interactions. -

    -

    The interactions have 2 components. The first is -Ball-Melrose lubrication terms via the formulas in (Ball and -Melrose) -

    -
    -
    -

    which represents the dissipation W between two nearby particles due to -their relative velocities in the presence of a background solvent with -viscosity mu. Note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. -

    -

    The Asq (squeeze) term is the strongest and is included as long as -flagHI is set to 1 (default). It scales as 1/gap where gap is the -separation between the surfaces of the 2 particles. The Ash (shear) -and Apu (pump) terms are only included if flaglog is set to 1. They -are the next strongest interactions, and the only other singular -interaction, and scale as log(gap). Note that flaglog = 1 and -flagHI = 0 is invalid, and will result in a warning message, after -which flagHI will be set to 1. The Atw (twist) term is currently not -included. It is typically a very small contribution to the lubrication -forces. -

    -

    The flagHI and flagVF settings are optional. Neither should be -used, or both must be defined. -

    -

    Cutinner sets the minimum center-to-center separation that will be -used in calculations irrespective of the actual separation. Cutoff -is the maximum center-to-center separation at which an interaction is -computed. Using a cutoff less than 3 radii is recommended if -flaglog is set to 1. -

    -

    The other component is due to the Fast Lubrication Dynamics (FLD) -approximation, described in (Kumar). The equation being -solved to balance the forces and torques is -

    -
    -
    -

    where U represents the velocities and angular velocities of the -particles, U^infty represents the velocities and the angular -velocities of the undisturbed fluid, and E^infty represents the rate -of strain tensor of the undisturbed fluid flow with viscosity -mu. Again, note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. Volume fraction -corrections to R_FU are included if flagVF is set to 1 (default). -

    -

    Frest represents the forces and torques due to all other types of -interactions, e.g. Brownian, electrostatic etc. Note that this -algorithm neglects the inertial terms, thereby removing the -restriction of resolving the small interial time scale, which may not -be of interest for colloidal particles. This pair style solves for -the velocity such that the hydrodynamic force balances all other types -of forces, thereby resulting in a net zero force (zero inertia limit). -When defining this pair style, it must be defined last so that when -this style is invoked all other types of forces have already been -computed. For the same reason, it won't work if additional non-pair -styles are defined (such as bond or Kspace forces) as they are -calculated in LAMMPS after the pairwise interactions have been -computed. -

    -

    IMPORTANT NOTE: When using these styles, the these pair styles are -designed to be used with implicit time integration and a -correspondingly larger timestep. Thus either fix -nve/noforce should be used for spherical -particles defined via atom_style sphere or fix -nve/asphere/noforce should be used for -spherical particles defined via atom_style -ellipsoid. This is because the velocity and angular -momentum of each particle is set by the pair style, and should not be -reset by the time integration fix. -

    -

    Style lubricateU requires monodisperse spherical particles; style -lubricateU/poly allows for polydisperse spherical particles. -

    -

    If the suspension is sheared via the fix deform -command then the pair style uses the shear rate to adjust the -hydrodynamic interactions accordingly. Volume changes due to fix -deform are accounted for when computing the volume fraction -corrections to R_FU. -

    -

    When computing the volume fraction corrections to R_FU, the presence -of walls (whether moving or stationary) will affect the volume -fraction available to colloidal particles. This is currently accounted -for with the following types of walls: wall/lj93, -wall/lj126, wall/colloid, and -"wall/harmonic_fix_wall.html". For these wall styles, the correct -volume fraction will be used when walls do not coincide with the box -boundary, as well as when walls move and thereby cause a change in the -volume fraction. To use these wall styles with pair_style lubricateU -or lubricateU/poly, the fld yes option must be specified in the -fix wall command. -

    -

    Since lubrication forces are dissipative, it is usually desirable to -thermostat the system at a constant temperature. If Brownian motion -(at a constant temperature) is desired, it can be set using the -pair_style brownian command. These pair styles -and the brownian style should use consistent parameters for mu, -flaglog, flagfld, cutinner, cutoff, flagHI and flagVF. -

    -
    - -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • cutinner (distance units) -
    • cutoff (distance units) -
    -

    The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is geometric. See -the "pair_modify" command for details. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Currently, these pair styles assume that all other types of -forces/torques on the particles have been already been computed when -it is invoked. This requires this style to be defined as the last of -the pair styles, and that no fixes apply additional constraint forces. -One exception is the fix wall/colloid commands, which -has an "fld" option to apply their wall forces correctly. -

    -

    Only spherical monodisperse particles are allowed for pair_style -lubricateU. -

    -

    Only spherical particles are allowed for pair_style lubricateU/poly. -

    -

    For sheared suspensions, it is assumed that the shearing is done in -the xy plane, with x being the velocity direction and y being the -velocity-gradient direction. In this case, one must use fix -deform with the same rate of shear (erate). -

    -

    Related commands: -

    -

    pair_coeff, pair_style -lubricate -

    -

    Default: -

    -

    The default settings for the optional args are flagHI = 1 and flagVF = -1. -

    -
    - - - -

    (Ball) Ball and Melrose, Physica A, 247, 444-472 (1997). -

    - - -

    (Kumar) Kumar and Higdon, Phys Rev E, 82, 051401 (2010). -

    - diff --git a/doc/doc2/pair_meam.html b/doc/doc2/pair_meam.html deleted file mode 100644 index 3a8f578f47..0000000000 --- a/doc/doc2/pair_meam.html +++ /dev/null @@ -1,383 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style meam command -

    -

    Syntax: -

    -
    pair_style meam 
-
    -

    Examples: -

    -
    pair_style meam
-pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
-pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni 
-
    -

    Description: -

    -

    NOTE: The behavior of the MEAM potential for alloy systems has changed -as of November 2010; see description below of the mixture_ref_t -parameter -

    -

    Style meam computes pairwise interactions for a variety of materials -using modified embedded-atom method (MEAM) potentials -(Baskes). Conceptually, it is an extension to the original -EAM potentials which adds angular forces. It is -thus suitable for modeling metals and alloys with fcc, bcc, hcp and -diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. -

    -

    In the MEAM formulation, the total energy E of a system of atoms is -given by: -

    -
    -
    -

    where F is the embedding energy which is a function of the atomic -electron density rho, and phi is a pair potential interaction. The -pair interaction is summed over all neighbors J of atom I within the -cutoff distance. As with EAM, the multi-body nature of the MEAM -potential is a result of the embedding energy term. Details of the -computation of the embedding and pair energies, as implemented in -LAMMPS, are given in (Gullet) and references therein. -

    -

    The various parameters in the MEAM formulas are listed in two files -which are specified by the pair_coeff command. -These are ASCII text files in a format consistent with other MD codes -that implement MEAM potentials, such as the serial DYNAMO code and -Warp. Several MEAM potential files with parameters for different -materials are included in the "potentials" directory of the LAMMPS -distribution with a ".meam" suffix. All of these are parameterized in -terms of LAMMPS metal units. -

    -

    Note that unlike for other potentials, cutoffs for MEAM potentials are -not set in the pair_style or pair_coeff command; they are specified in -the MEAM potential files themselves. -

    -

    Only a single pair_coeff command is used with the meam style which -specifies two MEAM files and the element(s) to extract information -for. The MEAM elements are mapped to LAMMPS atom types by specifying -N additional arguments after the 2nd filename in the pair_coeff -command, where N is the number of LAMMPS atom types: -

    -
    • MEAM library file -
    • Elem1, Elem2, ... -
    • MEAM parameter file -
    • N element names = mapping of MEAM elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential files. -

    -

    As an example, the potentials/library.meam file has generic MEAM -settings for a variety of elements. The potentials/sic.meam file has -specific parameter settings for a Si and C alloy system. If your -LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, -and the 4th to be C, you would use the following pair_coeff command: -

    -
    pair_coeff * * library.meam Si C sic.meam Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The two filenames are for the library and parameter file respectively. -The Si and C arguments (between the file names) are the two elements -for which info will be extracted from the library file. The first -three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si -element. The final C argument maps LAMMPS atom type 4 to the MEAM C -element. -

    -

    If the 2nd filename is specified as NULL, no parameter file is read, -which simply means the generic parameters in the library file are -used. Use of the NULL specification for the parameter file is -discouraged for systems with more than a single element type -(e.g. alloys), since the parameter file is expected to set element -interaction terms that are not captured by the information in the -library file. -

    -

    If a mapping value is specified as NULL, the mapping is not performed. -This can be used when a meam potential is used as part of the -hybrid pair style. The NULL values are placeholders for atom types -that will be used with other potentials. -

    -

    The MEAM library file provided with LAMMPS has the name -potentials/library.meam. It is the "meamf" file used by other MD -codes. Aside from blank and comment lines (start with #) which can -appear anywhere, it is formatted as a series of entries, each of which -has 19 parameters and can span multiple lines: -

    -

    elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub, -t0, t1, t2, t3, rozero, ibar -

    -

    The "elt" and "lat" parameters are text strings, such as elt = Si or -Cu and lat = dia or fcc. Because the library file is used by Fortran -MD codes, these strings may be enclosed in single quotes, but this is -not required. The other numeric parameters match values in the -formulas above. The value of the "elt" string is what is used in the -pair_coeff command to identify which settings from the library file -you wish to read in. There can be multiple entries in the library -file with the same "elt" value; LAMMPS reads the 1st matching entry it -finds and ignores the rest. -

    -

    Other parameters in the MEAM library file correspond to single-element -potential parameters: -

    -
    lat      = lattice structure of reference configuration
-z        = number of nearest neighbors in the reference structure
-ielement = atomic number
-atwt     = atomic weight
-alat     = lattice constant of reference structure
-esub     = energy per atom (eV) in the reference structure at equilibrium
-asub     = "A" parameter for MEAM (see e.g. (Baskes)) 
-
    -

    The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the -standard MEAM parameters in the literature (Baskes) (the b -parameters are the standard beta parameters). The rozero parameter is -an element-dependent density scaling that weights the reference -background density (see e.g. equation 4.5 in (Gullet)) and -is typically 1.0 for single-element systems. The ibar parameter -selects the form of the function G(Gamma) used to compute the electron -density; options are -

    -
       0 => G = sqrt(1+Gamma)
-   1 => G = exp(Gamma/2)
-   2 => not implemented 
-   3 => G = 2/(1+exp(-Gamma))
-   4 => G = sqrt(1+Gamma)
-  -5 => G = +-sqrt(abs(1+Gamma)) 
-
    -

    If used, the MEAM parameter file contains settings that override or -complement the library file settings. Examples of such parameter -files are in the potentials directory with a ".meam" suffix. Their -format is the same as is read by other Fortran MD codes. Aside from -blank and comment lines (start with #) which can appear anywhere, each -line has one of the following forms. Each line can also have a -trailing comment (starting with #) which is ignored. -

    -
    keyword = value
-keyword(I) = value
-keyword(I,J) = value
-keyword(I,J,K) = value 
-
    -

    The recognized keywords are as follows: -

    -

    Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr, -augt1, gsmooth_factor, re -

    -

    where -

    -
    rc          = cutoff radius for cutoff function; default = 4.0
-delr        = length of smoothing distance for cutoff function; default = 0.1
-rho0(I)     = relative density for element I (overwrites value
-              read from meamf file)
-Ec(I,J)     = cohesive energy of reference structure for I-J mixture
-delta(I,J)  = heat of formation for I-J alloy; if Ec_IJ is input as
-              zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
-alpha(I,J)  = alpha parameter for pair potential between I and J (can
-              be computed from bulk modulus of reference structure
-re(I,J)     = equilibrium distance between I and J in the reference
-              structure
-Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened 
-              by K (I<=J); default = 2.8
-Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened 
-              by K (I<=J); default = 2.0
-lattce(I,J) = lattice structure of I-J reference structure:
-                dia = diamond (interlaced fcc for alloy)
-                fcc = face centered cubic
-                bcc = body centered cubic
-                dim = dimer 
-                b1  = rock salt (NaCl structure)
-		hcp = hexagonal close-packed
-		c11 = MoSi2 structure
-		l12 = Cu3Au structure (lower case L, followed by 12)
-                b2  = CsCl structure (interpenetrating simple cubic)
-nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
-              I-J pair (see for example (Lee)).  
-                0 = second-nearest neighbor formulation off
-                1 = second-nearest neighbor formulation on
-                default = 0
-attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
-                default = 0            
-repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
-                default = 0     
-zbl(I,J)    = blend the MEAM I-J pair potential with the ZBL potential for small 
-              atom separations (ZBL) 
-                default = 1       
-gsmooth_factor  = factor determining the length of the G-function smoothing
-                  region; only significant for ibar=0 or ibar=4.
-                      99.0 = short smoothing region, sharp step
-                      0.5  = long smoothing region, smooth step
-                      default = 99.0
-augt1           = integer flag for whether to augment t1 parameter by
-                  3/5*t3 to account for old vs. new meam formulations;
-                    0 = don't augment t1
-                    1 = augment t1
-                    default = 1 
-ialloy          = integer flag to use alternative averaging rule for t parameters,
-                  for comparison with the DYNAMO MEAM code
-                    0 = standard averaging (matches ialloy=0 in DYNAMO)
-                    1 = alternative averaging (matches ialloy=1 in DYNAMO)
-                    2 = no averaging of t (use single-element values)
-                    default = 0
-mixture_ref_t   = integer flag to use mixture average of t to compute the background
-                  reference density for alloys, instead of the single-element values
-                  (see description and warning elsewhere in this doc page)
-                    0 = do not use mixture averaging for t in the reference density
-                    1 = use mixture averaging for t in the reference density
-                    default = 0 
-erose_form      = integer value to select the form of the Rose energy function 
-                  (see description below).
-                    default = 0
-emb_lin_neg     = integer value to select embedding function for negative densities
-                    0 = F(rho)=0
-                    1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
-                    default = 0
-bkgd_dyn        = integer value to select background density formula
-                    0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
-                    1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
-                    default = 0 
-
    -

    Rc, delr, re are in distance units (Angstroms in the case of metal -units). Ec and delta are in energy units (eV in the case of metal -units). -

    -

    Each keyword represents a quantity which is either a scalar, vector, -2d array, or 3d array and must be specified with the correct -corresponding array syntax. The indices I,J,K each run from 1 to N -where N is the number of MEAM elements being used. -

    -

    Thus these lines -

    -
    rho0(2) = 2.25
-alpha(1,2) = 4.37 
-
    -

    set rho0 for the 2nd element to the value 2.25 and set alpha for the -alloy interaction between elements 1 and 2 to 4.37. -

    -

    The augt1 parameter is related to modifications in the MEAM -formulation of the partial electron density function. In recent -literature, an extra term is included in the expression for the -third-order density in order to make the densities orthogonal (see for -example (Wang), equation 3d); this term is included in the -MEAM implementation in lammps. However, in earlier published work -this term was not included when deriving parameters, including most of -those provided in the library.meam file included with lammps, and to -account for this difference the parameter t1 must be augmented by -3/5*t3. If augt1=1, the default, this augmentation is done -automatically. When parameter values are fit using the modified -density function, as in more recent literature, augt1 should be set to -0. -

    -

    The mixture_ref_t parameter is available to match results with those -of previous versions of lammps (before January 2011). Newer versions -of lammps, by default, use the single-element values of the t -parameters to compute the background reference density. This is the -proper way to compute these parameters. Earlier versions of lammps -used an alloy mixture averaged value of t to compute the background -reference density. Setting mixture_ref_t=1 gives the old behavior. -WARNING: using mixture_ref_t=1 will give results that are demonstrably -incorrect for second-neighbor MEAM, and non-standard for -first-neighbor MEAM; this option is included only for matching with -previous versions of lammps and should be avoided if possible. -

    -

    The parameters attrac and repuls, along with the integer selection -parameter erose_form, can be used to modify the Rose energy function -used to compute the pair potential. This function gives the energy of -the reference state as a function of interatomic spacing. The form of -this function is: -

    -
    astar = alpha * (r/re - 1.d0)
-if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar) 
-if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
-if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
-a3 = repuls, astar < 0
-a3 = attrac, astar >= 0 
-
    -

    Most published MEAM parameter sets use the default values attrac=repulse=0. -Setting repuls=attrac=delta corresponds to the form used in several -recent published MEAM parameter sets, such as (Vallone) -

    -

    NOTE: The default form of the erose expression in LAMMPS was corrected -in March 2009. The current version is correct, but may show different -behavior compared with earlier versions of lammps with the attrac -and/or repuls parameters are non-zero. To obtain the previous default -form, use erose_form = 1 (this form does not seem to appear in the -literature). An alternative form (see e.g. (Lee2)) is -available using erose_form = 2. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS with -user-specifiable parameters as described above. You never need to -specify a pair_coeff command with I != J arguments for this style. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the MEAM package. It is only enabled if LAMMPS -was built with that package, which also requires the MEAM library be -built and linked with LAMMPS. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_style eam, -pair_style meam/spline -

    -

    Default: none -

    -
    - - - -

    (Baskes) Baskes, Phys Rev B, 46, 2727-2742 (1992). -

    - - -

    (Gullet) Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). -This report may be accessed on-line via this link. -

    - - - - -

    (Lee) Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000). -

    - - -

    (Lee2) Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001). -

    - - -

    (Valone) Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006). -

    - - -

    (Wang) Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004). -

    - - -

    (ZBL) J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges -of Ions in Matter", Vol 1, 1985, Pergamon Press. -

    - diff --git a/doc/doc2/pair_meam_spline.html b/doc/doc2/pair_meam_spline.html deleted file mode 100644 index e1a17d7b54..0000000000 --- a/doc/doc2/pair_meam_spline.html +++ /dev/null @@ -1,152 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style meam/spline -

    -

    pair_style meam/spline/omp -

    -

    Syntax: -

    -
    pair_style meam/spline 
-
    -

    Examples: -

    -
    pair_style meam/spline
-pair_coeff * * Ti.meam.spline Ti
-pair_coeff * * Ti.meam.spline Ti Ti Ti 
-
    -

    Description: -

    -

    The meam/spline style computes pairwise interactions for metals -using a variant of modified embedded-atom method (MEAM) potentials -(Lenosky). The total energy E is given by -

    -
    -
    -

    where rho_i is the density at atom I, theta_jik is the angle between -atoms J, I, and K centered on atom I. The five functions Phi, U, rho, -f, and g are represented by cubic splines. -

    -

    The cutoffs and the coefficients for these spline functions are listed -in a parameter file which is specified by the -pair_coeff command. Parameter files for different -elements are included in the "potentials" directory of the LAMMPS -distribution and have a ".meam.spline" file suffix. All of these -files are parameterized in terms of LAMMPS metal units. -

    -

    Note that unlike for other potentials, cutoffs for spline-based MEAM -potentials are not set in the pair_style or pair_coeff command; they -are specified in the potential files themselves. -

    -

    Unlike the EAM pair style, which retrieves the atomic mass from the -potential file, the spline-based MEAM potentials do not include mass -information; thus you need to use the mass command to -specify it. -

    -

    Only a single pair_coeff command is used with the meam/spline style -which specifies a potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of spline-based MEAM elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine the Ti.meam.spline file has values for Ti. If -your LAMMPS simulation has 3 atoms types and they are all to be -treated with this potentials, you would use the following pair_coeff -command: -

    -
    pair_coeff * * Ti.meam.spline Ti Ti Ti 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element -in the potential file. If a mapping value is specified as NULL, the -mapping is not performed. This can be used when a meam/spline -potential is used as part of the hybrid pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. -

    -

    IMPORTANT NOTE: The meam/spline style currently supports only -single-element MEAM potentials. It may be extended for alloy systems -in the future. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    The current version of this pair style does not support multiple -element types or mixing. It has been designed for pure elements only. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    The meam/spline pair style does not write its information to binary -restart files, since it is stored in an external -potential parameter file. Thus, you need to re-specify the pair_style -and pair_coeff commands in an input script that reads a restart file. -

    -

    The meam/spline pair style can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    This pair style is only enabled if LAMMPS was built with the USER-MISC -package. See the Making LAMMPS section -for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_style meam -

    -

    Default: none -

    -
    - - - -

    (Lenosky) Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, -Kress, Modelling Simulation Materials Science Enginerring, 8, 825 -(2000). -

    - diff --git a/doc/doc2/pair_meam_sw_spline.html b/doc/doc2/pair_meam_sw_spline.html deleted file mode 100644 index 391a28686d..0000000000 --- a/doc/doc2/pair_meam_sw_spline.html +++ /dev/null @@ -1,146 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style meam/sw/spline -

    -

    pair_style meam/sw/spline/omp -

    -

    Syntax: -

    -
    pair_style meam/sw/spline 
-
    -

    Examples: -

    -
    pair_style meam/sw/spline
-pair_coeff * * Ti.meam.sw.spline Ti
-pair_coeff * * Ti.meam.sw.spline Ti Ti Ti 
-
    -

    Description: -

    -

    The meam/sw/spline style computes pairwise interactions for metals -using a variant of modified embedded-atom method (MEAM) potentials -(Lenosky) with an additional Stillinger-Weber (SW) term -(Stillinger) in the energy. This form of the potential -was first proposed by Nicklas, Fellinger, and Park -(Nicklas). We refer to it as MEAM+SW. The total energy E -is given by -

    -
    -
    -

    where rho_I is the density at atom I, theta_JIK is the angle between -atoms J, I, and K centered on atom I. The seven functions -Phi, F, G, U, rho, f, and g are represented by cubic splines. -

    -

    The cutoffs and the coefficients for these spline functions are listed -in a parameter file which is specified by the -pair_coeff command. Parameter files for different -elements are included in the "potentials" directory of the LAMMPS -distribution and have a ".meam.sw.spline" file suffix. All of these -files are parameterized in terms of LAMMPS metal units. -

    -

    Note that unlike for other potentials, cutoffs for spline-based -MEAM+SW potentials are not set in the pair_style or pair_coeff -command; they are specified in the potential files themselves. -

    -

    Unlike the EAM pair style, which retrieves the atomic mass from the -potential file, the spline-based MEAM+SW potentials do not include -mass information; thus you need to use the mass command to -specify it. -

    -

    Only a single pair_coeff command is used with the meam/sw/spline style -which specifies a potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of spline-based MEAM+SW elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine the Ti.meam.sw.spline file has values for Ti. -If your LAMMPS simulation has 3 atoms types and they are all to be -treated with this potential, you would use the following pair_coeff -command: -

    -

    pair_coeff * * Ti.meam.sw.spline Ti Ti Ti -

    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element -in the potential file. If a mapping value is specified as NULL, the -mapping is not performed. This can be used when a meam/sw/spline -potential is used as part of the hybrid pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. -

    -

    IMPORTANT NOTE: The meam/sw/spline style currently supports only -single-element MEAM+SW potentials. It may be extended for alloy -systems in the future. -

    -

    Example input scripts that use this pair style are provided -in the examples/USER/misc/meam_sw_spline directory. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    The pair style does not support multiple element types or mixing. -It has been designed for pure elements only. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    The meam/sw/spline pair style does not write its information to -binary restart files, since it is stored in an external -potential parameter file. Thus, you need to re-specify the pair_style -and pair_coeff commands in an input script that reads a restart file. -

    -

    The meam/sw/spline pair style can only be used via the pair -keyword of the run_style respa command. They do not -support the inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    This pair style is only enabled if LAMMPS was built with the USER-MISC package. -See the Making LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_style meam, -pair_style meam/spline -

    -

    Default: none -

    -
    - - - -

    (Lenosky) Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, -Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000). -

    - - -

    (Stillinger) Stillinger, Weber, Phys. Rev. B 31, 5262 (1985). -

    - - -

    (Nicklas) -The spline-based MEAM+SW format was first devised and used to develop -potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger, -and Hyoungki Park at The Ohio State University. -

    - diff --git a/doc/doc2/pair_mgpt.html b/doc/doc2/pair_mgpt.html deleted file mode 100644 index 609695784c..0000000000 --- a/doc/doc2/pair_mgpt.html +++ /dev/null @@ -1,229 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style mgpt command -

    -

    Syntax: -

    -
    pair_style mgpt 
-
    -

    Examples: -

    -
    pair_style mgpt
-pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega 
-cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
-cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
-pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
-pair_coeff * * parmin potin Omega volpress yes nbody 12 
-
    -

    Description: -

    -

    Within DFT quantum mechanics, generalized pseudopotential theory (GPT) -(Moriarty1) provides a first-principles approach to -multi-ion interatomic potentials in d-band transition metals, with a -volume-dependent, real-space total-energy functional for the N-ion -elemental bulk material in the form -

    -
    -
    -

    where the prime on each summation sign indicates the exclusion of all -self-interaction terms from the summation. The leading volume term -E_vol as well as the two-ion central-force pair potential v_2 and the -three- and four-ion angular-force potentials, v_3 and v_4, depend -explicitly on the atomic volume Omega, but are structure independent -and transferable to all bulk ion configurations, either ordered or -disordered, and with of without the presence of point and line -defects. The simplified model GPT or MGPT (Moriarty2, -Moriarty3), which retains the form of E_tot and permits -more efficient large-scale atomistic simulations, derives from the GPT -through a series of systematic approximations applied to E_vol and the -potentials v_n that are valid for mid-period transition metals with -nearly half-filled d bands. -

    -

    Both analytic (Moriarty2) and matrix -(Moriarty3) representations of MGPT have been developed. -In the more general matrix representation, which can also be applied -to f-band actinide metals and permits both canonical and non-canonical -d/f bands, the multi-ion potentials are evaluated on the fly during a -simulation through d- or f-state matrix multiplication, and the forces -that move the ions are determined analytically. Fast matrix-MGPT -algorithms have been developed independently by Glosli -(Glosli, Moriarty3) and by Oppelstrup -(Oppelstrup) -

    -

    The mgpt pair style calculates forces, energies, and the total -energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. -Input potential and control data are entered through the -pair_coeff command. Each material treated requires -input parmin and potin potential files, as shown in the above -examples, as well as specification by the user of the initial atomic -volume Omega through pair_coeff. At the beginning of a time step in -any simulation, the total volume of the simulation cell V should -always be equal to Omega*N, where N is the number of metal ions -present, taking into account the presence of any vacancies and/or -interstitials in the case of a solid. In a constant-volume -simulation, which is the normal mode of operation for the mgpt pair -style, Omega, V and N all remain constant throughout the simulation -and thus are equal to their initial values. In a constant-stress -simulation, the cell volume V will change (slowly) as the simulation -proceeds. After each time step, the atomic volume should be updated -by the code as Omega = V/N. In addition, the volume term E_vol and -the potentials v_2, v_3 and v_4 have to be removed at the end of the -time step, and then respecified at the new value of Omega. In all -smulations, Omega must remain within the defined volume range for -E_vol and the potentials for the given material. -

    -

    The default option volpress yes in the pair_coeff -command includes all volume derivatives of E_tot required to calculate -the stress tensor and pressure correctly. The option volpress no -disregards the pressure contribution resulting from the volume term -E_vol, and can be used for testing and analysis purposes. The -additional optional variable nbody controls the specific terms in -E_tot that are calculated. The default option and the normal option -for mid-period transition and actinide metals is nbody 1234 for which -all four terms in E_tot are retained. The option nbody 12, for -example, retains only the volume term and the two-ion pair potential -term and can be used for GPT series-end transition metals that can be -well described without v_3 and v_4. The nbody option can also be used -to test or analyze the contribution of any of the four terms in E_tot -to a given calculated property. -

    -

    The mgpt pair style makes extensive use of matrix algebra and -includes optimized kernels for the BlueGene/Q architecture and the -Intel/AMD (x86) architectures. When compiled with the appropriate -compiler and compiler switches (-msse3 on x86, and using the IBM XL -compiler on BG/Q), these optimized routines are used automatically. -For BG/Q machines, building with the default Makefile for that -architecture (e.g., "make bgq") should enable the optimized algebra -routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt -(build with "make mpi_fastmgpt") enables the fast algebra routines. -The user will be informed in the output files of the matrix kernels in -use. To further improve speed, on x86 the option precision single can -be added to the pair_coeff command line, which -improves speed (up to a factor of two) at the cost of doing matrix -calculations with 7 digit precision instead of the default 16. For -consistency the default option can be specified explicitly by the -option precision double. -

    -

    All remaining potential and control data are contained with the parmin -and potin files, including cutoffs, atomic mass, and other basic MGPT -variables. Specific MGPT potential data for the transition metals -tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), -and vanadium (V6.1 potentials) are contained in the LAMMPS potentials -directory. The stored files are, respectively, Ta4.mgpt.parmin, -Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin, -Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and -V6.1.mgpt.potin . Useful corresponding informational "README" files -on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the -potentials directory. These latter files indicate the volume mesh and -range for each potential and give appropriate references for the -potentials. It is expected that MGPT potentials for additional -materials will be added over time. -

    -

    Useful example MGPT scripts are given in the examples/USER/mgpt -directory. These scripts show the necessary steps to perform -constant-volume calculations and simulations. It is strongly -recommended that the user work through and understand these examples -before proceeding to more complex simulations. -

    -

    IMPORTANT NOTE: For good performance, LAMMPS should be built with the -compiler flags "-O3 -msse3 -funroll-loops" when including this pair -style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example -machine Makefile with these options included as part of a standard MPI -build. Note that as-is it will build with whatever low-level compiler -(g++, icc, etc) is the default for your MPI installation. -

    -
    - -

    Mixing, shift, table tail correction, restart: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -needs to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the USER-MGPT package and is only enabled -if LAMMPS is built with that package. See the Making -LAMMPS section for more info. -

    -

    The MGPT potentials require the newtion setting to be -"on" for pair style interactions. -

    -

    The stored parmin and potin potential files provided with LAMMPS in -the "potentials" directory are written in Rydberg atomic units, with -energies in Rydbergs and distances in Bohr radii. The mgpt pair -style converts Rydbergs to Hartrees to make the potential files -compatible with LAMMPS electron units. -

    -

    The form of E_tot used in the mgpt pair style is only appropriate -for elemental bulk solids and liquids. This includes solids with -point and extended defects such as vacancies, interstitials, grain -boundaries and dislocations. Alloys and free surfaces, however, -require significant modifications, which are not included in the -mgpt pair style. Likewise, the hybrid pair style is not allowed, -where MGPT would be used for some atoms but not for others. -

    -

    Electron-thermal effects are not included in the standard MGPT -potentials provided in the "potentials" directory, where the -potentials have been constructed at zero electron temperature. -Physically, electron-thermal effects may be important in 3d (e.g., V) -and 4d (e.g., Mo) transition metals at high temperatures near melt and -above. It is expected that temperature-dependent MGPT potentials for -such cases will be added over time. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: -

    -

    The options defaults for the pair_coeff command are -volpress yes, nbody 1234, and precision double. -

    -
    - - - -

    (Moriarty1) Moriarty, Physical Review B, 38, 3199 (1988). -

    - - -

    (Moriarty2) Moriarty, Physical Review B, 42, 1609 (1990). -Moriarty, Physical Review B 49, 12431 (1994). -

    - - -

    (Moriarty3) Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, -Journal of Materials Research, 21, 563 (2006). -

    - - -

    (Glosli) Glosli, unpublished, 2005. -Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference -Series, 46, 254 (2006). -

    - - -

    (Oppelstrup) Oppelstrup, unpublished, 2015. -Oppelstrup and Moriarty, to be published. -

    - diff --git a/doc/doc2/pair_mie.html b/doc/doc2/pair_mie.html deleted file mode 100644 index e5207cb232..0000000000 --- a/doc/doc2/pair_mie.html +++ /dev/null @@ -1,107 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style mie/cut command -

    -

    pair_style mie/cut/gpu command -

    -

    Syntax: -

    -
    pair_style mie/cut cutoff 
-
    -
    • cutoff = global cutoff for mie/cut interactions (distance units) -
    -

    Examples: -

    -
    pair_style mie/cut 10.0
-pair_coeff 1 1 0.72 3.40 23.00 6.66
-pair_coeff 2 2 0.30 3.55 12.65 6.00
-pair_coeff 1 2 0.46 3.32 16.90 6.31 
-
    -

    Description: -

    -

    The mie/cut style computes the Mie potential, given by -

    -
    -
    -

    Rc is the cutoff and C is a function that depends on the repulsive and -attractive exponents, given by: -

    -
    -
    -

    Note that for 12/6 exponents, C is equal to 4 and the formula is the -same as the standard Lennard-Jones potential. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • gammaR -
    • gammaA -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global -cutoff specified in the pair_style command is used. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the mie/cut pair styles can be mixed. -If not explicity defined, both the repulsive and attractive gamma -exponents for different atoms will be calculated following the same -mixing rule defined for distances. The default mix value is -geometric. See the "pair_modify" command for details. -

    -

    This pair style supports the pair_modify shift -option for the energy of the pair interaction. -

    -

    This pair style supports the pair_modify tail -option for adding a long-range tail correction to the energy and -pressure of the pair interaction. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style supports the use of the inner, middle, and outer -keywords of the run_style respa command, meaning the -pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the run_style command for -details. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Mie) G. Mie, Ann Phys, 316, 657 (1903). -

    - - -

    (Avendano) C. Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, -G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011). -

    - diff --git a/doc/doc2/pair_modify.html b/doc/doc2/pair_modify.html deleted file mode 100644 index 726f292286..0000000000 --- a/doc/doc2/pair_modify.html +++ /dev/null @@ -1,271 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_modify command -

    -

    Syntax: -

    -
    pair_modify keyword values ... 
-
    -
    • one or more keyword/value pairs may be listed - -
    • keyword = pair or shift or mix or table or table/disp or tabinner or tabinner/disp or tail or compute - -
        pair values = sub-style N special which wt1 wt2 wt3
-    sub-style = sub-style of pair hybrid
-    N = which instance of sub-style (only if sub-style is used multiple times)
-    special which wt1 wt2 wt3 = override special_bonds settings (optional)
-    which = lj/coul or lj or coul
-    w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
-  mix value = geometric or arithmetic or sixthpower
-  shift value = yes or no
-  table value = N
-    2^N = # of values in table
-  table/disp value = N
-    2^N = # of values in table
-  tabinner value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  tabinner/disp value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  tail value = yes or no
-  compute value = yes or no 
-
      - -
    -

    Examples: -

    -

    pair_modify shift yes mix geometric -pair_modify tail yes -pair_modify table 12 -pair_modify pair lj/cut compute no -pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0:pre -

    -

    Description: -

    -

    Modify the parameters of the currently defined pair style. Not all -parameters are relevant to all pair styles. -

    -

    If used, the pair keyword must appear first in the list of keywords. -It can only be used with the hybrid and -hybrid/overlay pair styles. It means that all the -following parameters will only be modified for the specified -sub-style. If the sub-style is defined multiple times, then an -additional numeric argument N must also be specified, which is a -number from 1 to M where M is the number of times the sub-style was -listed in the pair_style hybrid command. The extra -number indicates which instance of the sub-style the remaining -keywords will be applied to. Note that if the pair keyword is not -used, and the pair style is hybrid or hybrid/overlay, then all the -specified keywords will be applied to all sub-styles. -

    -

    The special keyword can only be used in conjunction with the pair -keyword and must directly follow it. It allows to override the -special_bonds settings for the specified sub-style. -More details are given below. -

    -

    The mix keyword affects pair coefficients for interactions between -atoms of type I and J, when I != J and the coefficients are not -explicitly set in the input script. Note that coefficients for I = J -must be set explicitly, either in the input script via the -"pair_coeff" command or in the "Pair Coeffs" section of the data -file. For some pair styles it is not necessary to -specify coefficients when I != J, since a "mixing" rule will create -them from the I,I and J,J settings. The pair_modify mix value -determines what formulas are used to compute the mixed coefficients. -In each case, the cutoff distance is mixed the same way as sigma. -

    -

    Note that not all pair styles support mixing. Also, some mix options -are not available for certain pair styles. See the doc page for -individual pair styles for those restrictions. Note also that the -pair_coeff command also can be to directly set -coefficients for a specific I != J pairing, in which case no mixing is -performed. -

    -

    mix geometric -

    -
    epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = sqrt(sigma_i * sigma_j) 
-
    -

    mix arithmetic -

    -
    epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = (sigma_i + sigma_j) / 2 
-
    -

    mix sixthpower -

    -
    epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
-             (sigma_i^6 + sigma_j^6)
-sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) 
-
    -

    The shift keyword determines whether a Lennard-Jones potential is -shifted at its cutoff to 0.0. If so, this adds an energy term to each -pairwise interaction which will be included in the thermodynamic -output, but does not affect pair forces or atom trajectories. See the -doc page for individual pair styles to see which ones support this -option. -

    -

    The table and table/disp keywords apply to pair styles with a -long-range Coulombic term or long-range dispersion term respectively; -see the doc page for individual styles to see which potentials support -these options. If N is non-zero, a table of length 2^N is -pre-computed for forces and energies, which can shrink their -computational cost by up to a factor of 2. The table is indexed via a -bit-mapping technique (Wolff) and a linear interpolation is -performed between adjacent table values. In our experiments with -different table styles (lookup, linear, spline), this method typically -gave the best performance in terms of speed and accuracy. -

    -

    The choice of table length is a tradeoff in accuracy versus speed. A -larger N yields more accurate force computations, but requires more -memory which can slow down the computation due to cache misses. A -reasonable value of N is between 8 and 16. The default value of 12 -(table of length 4096) gives approximately the same accuracy as the -no-table (N = 0) option. For N = 0, forces and energies are computed -directly, using a polynomial fit for the needed erfc() function -evaluation, which is what earlier versions of LAMMPS did. Values -greater than 16 typically slow down the simulation and will not -improve accuracy; values from 1 to 8 give unreliable results. -

    -

    The tabinner and tabinner/disp keywords set an inner cutoff above -which the pairwise computation is done by table lookup (if tables are -invoked), for the corresponding Coulombic and dispersion tables -discussed with the table and table/disp keywords. The smaller the -cutoff is set, the less accurate the table becomes (for a given number -of table values), which can require use of larger tables. The default -cutoff value is sqrt(2.0) distance units which means nearly all -pairwise interactions are computed via table lookup for simulations -with "real" units, but some close pairs may be computed directly -(non-table) for simulations with "lj" units. -

    -

    When the tail keyword is set to yes, certain pair styles will add -a long-range VanderWaals tail "correction" to the energy and pressure. -These corrections are bookkeeping terms which do not affect dynamics, -unless a constant-pressure simulation is being performed. See the doc -page for individual styles to see which support this option. These -corrections are included in the calculation and printing of -thermodynamic quantities (see the thermo_style -command). Their effect will also be included in constant NPT or NPH -simulations where the pressure influences the simulation box -dimensions (e.g. the fix npt and fix nph -commands). The formulas used for the long-range corrections come from -equation 5 of (Sun). -

    -

    IMPORTANT NOTE: The tail correction terms are computed at the -beginning of each run, using the current atom counts of each atom -type. If atoms are deleted (or lost) or created during a simulation, -e.g. via the fix gcmc command, the correction factors -are not re-computed. If you expect the counts to change dramatically, -you can break a run into a series of shorter runs so that the -correction factors are re-computed more frequently. -

    -

    Several additional assumptions are inherent in using tail corrections, -including the following: -

    -
    • The simulated system is a 3d bulk homogeneous liquid. This option -should not be used for systems that are non-liquid, 2d, have a slab -geometry (only 2d periodic), or inhomogeneous. - -
    • G(r), the radial distribution function (rdf), is unity beyond the -cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an -LJ fluid), and it is probably a good idea to verify this assumption by -checking the rdf. The rdf is not exactly unity beyond the cutoff for -each pair of interaction types, so the tail correction is necessarily -an approximation. - -

      The tail corrections are computed at the beginning of each simulation -run. If the number of atoms changes during the run, e.g. due to atoms -leaving the simulation domain, or use of the fix gcmc -command, then the corrections are not updates to relect the changed -atom count. If this is a large effect in your simulation, you should -break the long run into several short runs, so that the correction -factors are re-computed multiple times. -

      -
    • Thermophysical properties obtained from calculations with this option -enabled will not be thermodynamically consistent with the truncated -force-field that was used. In other words, atoms do not feel any LJ -pair interactions beyond the cutoff, but the energy and pressure -reported by the simulation include an estimated contribution from -those interactions. -
    -

    The compute keyword allows pairwise computations to be turned off, -even though a pair_style is defined. This is not -useful for running a real simulation, but can be useful for debugging -purposes or for performing a rerun simulation, when you -only wish to compute partial forces that do not include the pairwise -contribution. -

    -

    Two examples are as follows. First, this option allows you to perform -a simulation with pair_style hybrid with only a -subset of the hybrid sub-styles enabled. Second, this option allows -you to perform a simulation with only long-range interactions but no -short-range pairwise interactions. Doing this by simply not defining -a pair style will not work, because the -kspace_style command requires a Kspace-compatible -pair style be defined. -

    -
    - -
    Use of special keyword -
    -

    The special keyword allows to override the 1-2, 1-3, and 1-4 -exclusion settings for individual sub-styles of a -hybrid pair style. It requires 4 arguments similar -to the special_bonds command, which and -wt1,wt2,wt3. The which argument can be lj to change the -Lennard-Jones settings, coul to change the Coulombic settings, -or lj/coul to change both to the same set of 3 values. The wt1,wt2,wt3 -values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, -1-3, and 1-4 bond topology neighbors, respectively. The special -keyword can only be used in conjunction with the pair keyword -and has to directly follow it. -

    -

    IMPORTANT NOTE: The global settings specified by the -special_bonds command affect the construction of -neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) -exclude those pairs from the neighbor list entirely. Weights of 1.0 -store the neighbor with no weighting applied. Thus only global values -different from exactly 0.0 or 1.0 can be overridden and an error -is generated if the requested setting is not compatible with the -global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for -1.0 is usually a sufficient workaround in this case without causing -a significant error. -

    -
    - -

    Restrictions: none -

    -

    You cannot use shift yes with tail yes, since those are -conflicting options. You cannot use tail yes with 2d simulations. -

    -

    Related commands: -

    -

    pair_style, pair_coeff, -thermo_style -

    -

    Default: -

    -

    The option defaults are mix = geometric, shift = no, table = 12, -tabinner = sqrt(2.0), tail = no, and compute = yes. -

    -

    Note that some pair styles perform mixing, but only a certain style of -mixing. See the doc pages for individual pair styles for details. -

    -
    - - - -

    (Wolff) Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). -

    - - -

    (Sun) Sun, J Phys Chem B, 102, 7338-7364 (1998). -

    - diff --git a/doc/doc2/pair_morse.html b/doc/doc2/pair_morse.html deleted file mode 100644 index 58beb18f7f..0000000000 --- a/doc/doc2/pair_morse.html +++ /dev/null @@ -1,114 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style morse command -

    -

    pair_style morse/cuda command -

    -

    pair_style morse/gpu command -

    -

    pair_style morse/omp command -

    -

    pair_style morse/opt command -

    -

    Syntax: -

    -
    pair_style morse cutoff 
-
    -
    • cutoff = global cutoff for Morse interactions (distance units) -
    -

    Examples: -

    -
    pair_style morse 2.5
-pair_coeff * * 100.0 2.0 1.5
-pair_coeff 1 1 100.0 2.0 1.5 3.0 
-
    -

    Description: -

    -

    Style morse computes pairwise interactions with the formula -

    -
    -
    -

    Rc is the cutoff. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • D0 (energy units) -
    • alpha (1/distance units) -
    • r0 (distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global morse -cutoff is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    None of these pair styles support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    All of these pair styles support the pair_modify -shift option for the energy of the pair interaction. -

    -

    The pair_modify table options is not relevant for -the Morse pair styles. -

    -

    None of these pair styles support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    All of these pair styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_nb3b_harmonic.html b/doc/doc2/pair_nb3b_harmonic.html deleted file mode 100644 index 6d258736e1..0000000000 --- a/doc/doc2/pair_nb3b_harmonic.html +++ /dev/null @@ -1,129 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style nb3b/harmonic command -

    -

    pair_style nb3b/harmonic/omp command -

    -

    Syntax: -

    -
    pair_style nb3b/harmonic 
-
    -

    Examples: -

    -
    pair_style nb3b/harmonic
-pair_coeff * * MgOH.nb3bharmonic Mg O H 
-
    -

    Description: -

    -

    This pair style computes a nonbonded 3-body harmonic potential for the -energy E of a system of atoms as -

    -
    -
    -

    where theta_0 is the equilibrium value of the angle and K is a -prefactor. Note that the usual 1/2 factor is included in K. The form -of the potential is identical to that used in angle_style harmonic, -but in this case, the atoms do not need to be explicitly bonded. -

    -

    Only a single pair_coeff command is used with this style which -specifies a potential file with parameters for specified elements. -These are mapped to LAMMPS atom types by specifying N additional -arguments after the filename in the pair_coeff command, where N is the -number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine a file SiC.nb3b.harmonic has potential values -for Si and C. If your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be Si, and the 4th to be C, you would use the -following pair_coeff command: -

    -
    pair_coeff * * SiC.nb3b.harmonic Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the potential file. The final C argument maps LAMMPS atom -type 4 to the C element in the potential file. If a mapping value is -specified as NULL, the mapping is not performed. This can be used -when the potential is used as part of the hybrid pair style. The -NULL values are placeholders for atom types that will be used with -other potentials. An example of a pair_coeff command for use with the -hybrid pair style is: -

    -

    pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H -

    -

    Three-body nonbonded harmonic files in the potentials directory of -the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that -are not blank or comments (starting with #) define parameters for a -triplet of elements. -

    -

    Each entry has six arguments. The first three are atom types as -referenced in the LAMMPS input file. The first argument specifies the -central atom. The fourth argument indicates the K parameter. The -fifth argument indicates theta_0. The sixth argument indicates a -separation cutoff in Angstroms. -

    -

    For a given entry, if the second and third arguments are identical, -then the entry is for a cutoff for the distance between types 1 and 2 -(values for K and theta_0 are irrelevant in this case). -

    -

    For a given entry, if the first three arguments are all different, -then the entry is for the K and theta_0 parameters (the cutoff in -this case is irrelevant). -

    -

    It is not required that the potential file contain entries for all -of the elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    This pair style can only be used if LAMMPS was built with the MANYBODY -package (which it is by default). See the Making -LAMMPS section for more info on packages. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_nm.html b/doc/doc2/pair_nm.html deleted file mode 100644 index 809bdb3bd6..0000000000 --- a/doc/doc2/pair_nm.html +++ /dev/null @@ -1,183 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style nm/cut command -

    -

    pair_style nm/cut/coul/cut command -

    -

    pair_style nm/cut/coul/long command -

    -

    pair_style nm/cut/omp command -

    -

    pair_style nm/cut/coul/cut/omp command -

    -

    pair_style nm/cut/coul/long/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = nm/cut or nm/cut/coul/cut or nm/cut/coul/long - -
    • args = list of arguments for a particular style - -
        nm/cut args = cutoff
-    cutoff = global cutoff for Pair interactions (distance units)
-  nm/cut/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  nm/cut/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
      - -
    -

    Examples: -

    -
    pair_style nm/cut 12.0
-pair_coeff * * 0.01 5.4 8.0 7.0
-pair_coeff 1 1 0.01 4.4 7.0 6.0 
-
    -
    pair_style nm/cut/coul/cut 12.0 15.0
-pair_coeff * * 0.01 5.4 8.0 7.0
-pair_coeff 1 1 0.01 4.4 7.0 6.0 
-
    -
    pair_style nm/cut/coul/long 12.0 15.0
-pair_coeff * * 0.01 5.4 8.0 7.0
-pair_coeff 1 1 0.01 4.4 7.0 6.0 
-
    -

    Description: -

    -

    Style nm computes site-site interactions based on the N-M potential -by Clarke, mainly used for ionic liquids. A site can -represent a single atom or a united-atom site. The energy of an -interaction has the following form: -

    -
    -
    -

    Rc is the cutoff. -

    -

    Style nm/cut/coul/cut adds a Coulombic pairwise interaction given by -

    -
    -
    -

    where C is an energy-conversion constant, Qi and Qj are the charges on -the 2 atoms, and epsilon is the dielectric constant which can be set -by the dielectric command. If one cutoff is -specified in the pair_style command, it is used for both the NM and -Coulombic terms. If two cutoffs are specified, they are used as -cutoffs for the NM and Coulombic terms respectively. -

    -

    Styles nm/cut/coul/long compute the same -Coulombic interactions as style nm/cut/coul/cut except that an -additional damping factor is applied to the Coulombic term so it can -be used in conjunction with the kspace_style -command and its ewald or pppm option. The Coulombic cutoff -specified for this style means that pairwise interactions within this -distance are computed directly; interactions outside that distance are -computed in reciprocal space. -

    -

    For all of the nm pair styles, the following coefficients must -be defined for each pair of atoms types -via the pair_coeff command as in the -examples above, or in the data file or restart files read by the -read_data or read_restart -commands. -

    -
    • E0 (energy units) -
    • r0 (distance units) -
    • n (unitless) -
    • m (unitless) -
    • cutoff1 (distance units) -
    • cutoff2 (distance units) -
    -

    The latter 2 coefficients are optional. If not specified, the global -NM and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both NM -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the NM and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style nm, since it -has no Coulombic terms. -

    -

    For nm/cut/coul/long only the NM cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    All of the nm pair styles supports the -pair_modify shift option for the energy of the pair -interaction. -

    -

    The nm/cut/coul/long pair styles support the -pair_modify table option since they can tabulate -the short-range portion of the long-range Coulombic interaction. -

    -

    All of the nm pair styles support the pair_modify -tail option for adding a long-range tail correction to the energy and -pressure for the NM portion of the pair interaction. -

    -

    All of the nm pair styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    All of the nm pair styles can only be used via the pair keyword of -the run_style respa command. They do not support the -inner, middle, outer keywords. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -

    Restrictions: -

    -

    These pair styles are part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Clarke) Clarke and Smith, J Chem Phys, 84, 2290 (1986). -

    - diff --git a/doc/doc2/pair_none.html b/doc/doc2/pair_none.html deleted file mode 100644 index d6d1fedead..0000000000 --- a/doc/doc2/pair_none.html +++ /dev/null @@ -1,45 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style none command -

    -

    Syntax: -

    -
    pair_style none 
-
    -

    Examples: -

    -
    pair_style none 
-
    -

    Description: -

    -

    Using a pair style of none means pair forces are not computed. -

    -

    With this choice, the force cutoff is 0.0, which means that only atoms -within the neighbor skin distance (see the neighbor -command) are communicated between processors. You must insure the -skin distance is large enough to acquire atoms needed for computing -bonds, angles, etc. -

    -

    A pair style of none will also prevent pairwise neighbor lists from -being built. However if the neighbor style is bin, -data structures for binning are still allocated. If the neighbor skin -distance is small, then these data structures can consume a large -amount of memory. So you should either set the neighbor style to -nsq or set the skin distance to a larger value. -

    -

    Restrictions: none -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_peri.html b/doc/doc2/pair_peri.html deleted file mode 100644 index a505847a6f..0000000000 --- a/doc/doc2/pair_peri.html +++ /dev/null @@ -1,231 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style peri/pmb command -

    -

    pair_style peri/pmb/omp command -

    -

    pair_style peri/lps command -

    -

    pair_style peri/lps/omp command -

    -

    pair_style peri/ves command -

    -

    pair_style peri/eps command -

    -

    Syntax: -

    -
    pair_style style 
-
    -

    style = peri/pmb or peri/lps or peri/ves or peri/eps:ul -

    -

    Examples: -

    -
    pair_style peri/pmb
-pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 
-
    -
    pair_style peri/lps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 
-
    -
    pair_style peri/ves
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001 
-
    -
    pair_style peri/eps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43 
-
    -

    Description: -

    -

    The peridynamic pair styles implement material models that can be used -at the mescscopic and macroscopic scales. See this -document for an overview of LAMMPS commands -for Peridynamics modeling. -

    -

    Style peri/pmb implements the Peridynamic bond-based prototype -microelastic brittle (PMB) model. -

    -

    Style peri/lps implements the Peridynamic state-based linear -peridynamic solid (LPS) model. -

    -

    Style peri/ves implements the Peridynamic state-based linear -peridynamic viscoelastic solid (VES) model. -

    -

    Style peri/eps implements the Peridynamic state-based elastic-plastic -solid (EPS) model. -

    -

    The canonical papers on Peridynamics are (Silling 2000) -and (Silling 2007). The implementation of Peridynamics -in LAMMPS is described in (Parks). Also see the PDLAMMPS -user guide for -more details about its implementation. -

    -

    The peridynamic VES and EPS models in PDLAMMPS were implemented by -R. Rahman and J. T. Foster at University of Texas at San Antonio. The -original VES formulation is described in "(Mitchell2011)" and the -original EPS formulation is in "(Mitchell2011a)". Additional PDF docs -that describe the VES and EPS implementations are include in the -LAMMPS distro in doc/PDF/PDLammps_VES.pdf and -doc/PDF/PDLammps_EPS.pdf. For questions -regarding the VES and EPS models in LAMMPS you can contact R. Rahman -(rezwanur.rahman at utsa.edu). -

    -

    The following coefficients must be defined for each pair of atom types -via the pair_coeff command as in the examples above, -or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below. -

    -

    For the peri/pmb style: -

    -
    • c (energy/distance/volume^2 units) -
    • horizon (distance units) -
    • s00 (unitless) -
    • alpha (unitless) -
    -

    C is the effectively a spring constant for Peridynamic bonds, the -horizon is a cutoff distance for truncating interactions, and s00 and -alpha are used as a bond breaking criteria. The units of c are such -that c/distance = stiffness/volume^2, where stiffness is -energy/distance^2 and volume is distance^3. See the users guide for -more details. -

    -

    For the peri/lps style: -

    -
    • K (force/area units) -
    • G (force/area units) -
    • horizon (distance units) -
    • s00 (unitless) -
    • alpha (unitless) -
    -

    K is the bulk modulus and G is the shear modulus. The horizon is a -cutoff distance for truncating interactions, and s00 and alpha are -used as a bond breaking criteria. See the users guide for more -details. -

    -

    For the peri/ves style: -

    -
    • K (force/area units) -
    • G (force/area units) -
    • horizon (distance units) -
    • s00 (unitless) -
    • alpha (unitless) -
    • m_lambdai (unitless) -
    • m_taubi (unitless) -
    -

    K is the bulk modulus and G is the shear modulus. The horizon is a -cutoff distance for truncating interactions, and s00 and alpha are -used as a bond breaking criteria. m_lambdai and m_taubi are the -viscoelastic relaxation parameter and time constant, -respectively. m_lambdai varies within zero to one. For very small -values of m_lambdai the viscoelsatic model responds very similar to a -linear elastic model. For details please see the description in -"(Mtchell2011)". -

    -

    For the peri/eps style: -

    -

    K (force/area units) -G (force/area units) -horizon (distance units) -s00 (unitless) -alpha (unitless) -m_yield_stress (force/area units) -

    -

    K is the bulk modulus and G is the shear modulus. The horizon is a -cutoff distance and s00 and alpha are used as a bond breaking -criteria. m_yield_stress is the yield stress of the material. For -details please see the description in "(Mtchell2011a)". -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    These pair styles do not support the pair_modify -shift option. -

    -

    The pair_modify table and tail options are not -relevant for these pair styles. -

    -

    These pair styles write their information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    These pair styles can only be used via the pair keyword of the -run_style respa command. They do not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    All of these styles are part of the PERI package. They are only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Parks) Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), -777-783 (2008). -

    - - -

    (Silling 2000) Silling, J Mech Phys Solids, 48, 175-209 (2000). -

    - - -

    (Silling 2007) Silling, Epton, Weckner, Xu, Askari, J Elasticity, -88, 151-184 (2007). -

    - - -

    (Mitchell2011) Mitchell. A non-local, ordinary-state-based -viscoelasticity model for peridynamics. Sandia National Lab Report, -8064:1-28 (2011). -

    - - -

    (Mitchell2011a) Mitchell. A Nonlocal, Ordinary, State-Based -Plasticity Model for Peridynamics. Sandia National Lab Report, -3166:1-34 (2011). -

    - diff --git a/doc/doc2/pair_polymorphic.html b/doc/doc2/pair_polymorphic.html deleted file mode 100644 index 44bee3163e..0000000000 --- a/doc/doc2/pair_polymorphic.html +++ /dev/null @@ -1,245 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style polymorphic command -

    -

    Syntax: -

    -
    pair_style polymorphic 
-
    -

    style = polymorphic -

    -

    Examples: -

    -
    pair_style polymorphic
-pair_coeff * * TlBr_msw.polymorphic Tl Br
-pair_coeff * * AlCu_eam.polymorphic Al Cu
-pair_coeff * * GaN_tersoff.polymorphic Ga N
-pair_coeff * * GaN_sw.polymorphic GaN 
-
    -

    Description: -

    -

    The polymorphic pair style computes a 3-body free-form potential -(Zhou) for the energy E of a system of atoms as -

    -
    -
    -
    -
    -
    -
    -

    where I, J, K represent species of atoms i, j, and k, i_1, ..., i_N -represents a list of i's neighbors, delta_ij is a Direc constant -(i.e., delta_ij = 1 when i = j, and delta_ij = 0 otherwise), eta_ij is -similar constant that can be set either to eta_ij = delta_ij or eta_ij -= 1 - delta_ij depending on the potential type, U_IJ(r_ij), -V_IJ(r_ij), W_IK(r_ik) are pair functions, G_JIK(cos(theta)) is an -angular function, P_IK(delta r_jik) is a function of atomic spacing -differential delta r_jik = r_ij - xi_IJ*r_ik with xi_IJ being a -pair-dependent parameter, and F_IJ(X_ij) is a function of the local -environment variable X_ij. This generic potential is fully defined -once the constants eta_ij and xi_IJ, and the six functions U_IJ(r_ij), -V_IJ(r_ij), W_IK(r_ik), G_JIK(cos(theta)), P_IK(delta r_jik), and -F_IJ(X_ij) are given. Note that these six functions are all one -dimensional, and hence can be provided in an analytic or tabular -form. This allows users to design different potentials solely based on -a manipulation of these functions. For instance, the potential reduces -to Stillinger-Weber potential (SW) if we set -

    -
    -
    -

    The potential reduces to Tersoff types of potential -(Tersoff or Albe) if we set -

    -
    -
    -
    -
    -

    The potential reduces to Rockett-Tersoff (Wang) type if we set -

    -
    -
    -
    -
    -
    -
    -

    The potential becomes embedded atom method (Daw) if we set -

    -
    -
    -

    In the embedded atom method case, phi_IJ(r_ij) is the pair energy, -F_I(X) is the embedding energy, X is the local electron density, and -f_K(r) is the atomic electron density function. -

    -

    If the tabulated functions are created using the parameters of sw, -tersoff, and eam potentials, the polymorphic pair style will produce -the same global properties (energies and stresses) and the same forces -as the sw, tersoff, and eam pair styles. The polymorphic pair style -also produces the same atom properties (energies and stresses) as the -corresponding tersoff and eam pair styles. However, due to a different -partition of global properties to atom properties, the polymorphic -pair style will produce different atom properties (energies and -stresses) as the sw pair style. This does not mean that polymorphic -pair style is different from the sw pair style in this case. It just -means that the definitions of the atom energies and atom stresses are -different. -

    -

    Only a single pair_coeff command is used with the polymorphic style -which specifies an potential file for all needed elements. These are -mapped to LAMMPS atom types by specifying N additional arguments after -the filename in the pair_coeff command, where N is the number of -LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of Tersoff elements to atom types -
    -

    See the pair_coeff doc page for alternate ways to specify the path for -the potential file. Several files for polymorphic potentials are -included in the potentials dir of the LAMMPS distro. They have a -"poly" suffix. -

    -

    As an example, imagine the SiC_tersoff.polymorphic file has tabulated -functions for Si-C tersoff potential. If your LAMMPS simulation has 4 -atoms types and you want the 1st 3 to be Si, and the 4th to be C, you -would use the following pair_coeff command: -

    -
    pair_coeff * * SiC_tersoff.polymorphic Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom -types. The first three Si arguments map LAMMPS atom types 1,2,3 to the -Si element in the polymorphic file. The final C argument maps LAMMPS -atom type 4 to the C element in the polymorphic file. If a mapping -value is specified as NULL, the mapping is not performed. This can be -used when an polymorphic potential is used as part of the hybrid pair -style. The NULL values are placeholders for atom types that will be -used with other potentials. -

    -

    Potential files in the potentials directory of the LAMMPS distribution -have a ".poly" suffix. At the beginning of the files, an unlimited -number of lines starting with '#' are used to describe the potential -and are ignored by LAMMPS. The next line lists two numbers: -

    -
    ntypes eta 
-
    -

    Here ntypes represent total number of species defined in the potential -file, and eta = 0 or 1. The number ntypes must equal the total number -of different species defined in the pair_coeff command. When eta = 1, -eta_ij defined in the potential functions above is set to 1 - -delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines -each lists two numbers and a character string representing atomic -number, atomic mass, and name of the species of the ntypes elements: -

    -
    atomic_number atomic-mass element (1)
-atomic_number atomic-mass element (2)
-...
-atomic_number atomic-mass element (ntypes) 
-
    -

    The next ntypes*(ntypes+1)/2 lines contain two numbers: -

    -
    cut xi (1)
-cut xi (2)
-...
-cut xi (ntypes*(ntypes+1)/2) 
-
    -

    Here cut means the cutoff distance of the pair functions, xi is the -same as defined in the potential functions above. The -ntypes*(ntypes+1)/2 lines are related to the pairs according to the -sequence of first ii (self) pairs, i = 1, 2, ..., ntypes, and then -then ij (cross) pairs, i = 1, 2, ..., ntypes-1, and j = i+1, i+2, ..., -ntypes (i.e., the sequence of the ij pairs follows 11, 22, ..., 12, -13, 14, ..., 23, 24, ...). -

    -

    The final blocks of the potential file are the U, V, W, P, G, and F -functions are listed sequentially. First, U functions are given for -each of the ntypes*(ntypes+1)/2 pairs according to the sequence -described above. For each of the pairs, nr values are listed. Next, -similar arrays are given for V, W, and P functions. Then G functions -are given for all the ntypes*ntypes*ntypes ijk triplets in a natural -sequence i from 1 to ntypes, j from 1 to ntypes, and k from 1 to -ntypes (i.e., ijk = 111, 112, 113, ..., 121, 122, 123 ..., 211, 212, -...). Each of the ijk functions contains ng values. Finally, the F -functions are listed for all ntypes*(ntypes+1)/2 pairs, each -containing nx values. Either analytic or tabulated functions can be -specified. Currently, constant, exponential, sine and cosine analytic -functions are available which are specified with: constant c1 , where -f(x) = c1 exponential c1 c2 , where f(x) = c1 exp(c2*x) sine c1 c2 , -where f(x) = c1 sin(c2*x) cos c1 c2 , where f(x) = c1 cos(c2*x) -Tabulated functions are specified by spline n x1 x2, where n=number of -point, (x1,x2)=range and then followed by n values evaluated uniformly -over these argument ranges. The valid argument ranges of the -functions are between 0 <= r <= cut for the U(r), V(r), W(r) -functions, -cutmax <= delta_r <= cutmax for the P(delta_r) functions, --1 <= costheta <= 1 for the G(costheta) functions, and 0 <= X <= maxX -for the F(X) functions. -

    -

    Mixing, shift, table tail correction, restart: -

    -

    This pair styles does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write their information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -
    - -

    Restrictions: -

    -

    If using create_atoms command, atomic masses must be defined in the -input script. If using read_data, atomic masses must be defined in the -atomic structure data file. -

    -

    This pair style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package (which it is by default). See the -Making LAMMPS section for more info. -

    -

    This pair potential requires the newtion setting to be -"on" for pair interactions. -

    -

    The potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal units. You can use -any LAMMPS units, but you would need to create your own potential -files. -

    -

    Related commands: -

    -

    pair_coeff -

    -
    - - - -

    (Zhou) X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and -F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015). -

    - - -

    (SW) F. H. Stillinger-Weber, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985). -

    - - -

    (Tersoff) J. Tersoff, Phys. Rev. B, 39, 5566 (1989). -

    - - -

    (Albe) K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, -66, 035205 (2002). -

    - - -

    (Wang) J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991). -

    - - -

    (Daw) M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984). -

    - diff --git a/doc/doc2/pair_quip.html b/doc/doc2/pair_quip.html deleted file mode 100644 index 93096fca19..0000000000 --- a/doc/doc2/pair_quip.html +++ /dev/null @@ -1,102 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style quip command -

    -

    Syntax: -

    -
    pair_style quip 
-
    -

    Examples: -

    -
    pair_style      quip
-pair_coeff      * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
-pair_coeff      * * sw_example.xml "IP SW" 14 
-
    -

    Description: -

    -

    Style quip provides an interface for calling potential routines from -the QUIP package. QUIP is built separately, and then linked to -LAMMPS. The most recent version of the QUIP package can be downloaded -from GitHub: -https://github.com/libAtoms/QUIP. The -interface is chiefly intended to be used to run Gaussian Approximation -Potentials (GAP), which are described in the following publications: -(Bartok et al) and (PhD thesis of -Bartok). -

    -

    Only a single pair_coeff command is used with the quip style that -specifies a QUIP potential file containing the parameters of the -potential for all needed elements in XML format. This is followed by a -QUIP initialization string. Finally, the QUIP elements are mapped to -LAMMPS atom types by specifying N atomic numbers, where N is the -number of LAMMPS atom types: -

    -
    • QUIP filename -
    • QUIP initialization string -
    • N atomic numbers = mapping of QUIP elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    A QUIP potential is fully specified by the filename which contains the -parameters of the potential in XML format, the initialisation string, -and the map of atomic numbers. -

    -

    GAP potentials can be obtained from the Data repository section of -http://www.libatoms.org, where the -appropriate initialisation strings are also advised. The list of -atomic numbers must be matched to the LAMMPS atom types specified in -the LAMMPS data file or elsewhere. -

    -

    Two examples input scripts are provided in the examples/USER/quip -directory. -

    -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair style is part of the USER-QUIP package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    QUIP potentials are parametrized in electron-volts and Angstroms and -therefore should be used with LAMMPS metal units. -

    -

    Related commands: -

    -

    pair_coeff -

    -
    - - - -

    (Bartok_2010) AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical -Review Letters 104, 136403 (2010). -

    - - -

    (Bartok_PhD) A Bartok-Partay, PhD Thesis, University of Cambridge, -(2010). -

    - diff --git a/doc/doc2/pair_reax.html b/doc/doc2/pair_reax.html deleted file mode 100644 index 3b7aa08940..0000000000 --- a/doc/doc2/pair_reax.html +++ /dev/null @@ -1,218 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style reax command -

    -

    Syntax: -

    -
    pair_style reax hbcut hbnewflag tripflag precision 
-
    -
    • hbcut = hydrogen-bond cutoff (optional) (distance units) -
    • hbnewflag = use old or new hbond function style (0 or 1) (optional) -
    • tripflag = apply stabilization to all triple bonds (0 or 1) (optional) -
    • precision = precision for charge equilibration (optional) -
    -

    Examples: -

    -
    pair_style reax
-pair_style reax 10.0 0 1 1.0e-5
-pair_coeff * * ffield.reax 3 1 2 2
-pair_coeff * * ffield.reax 3 NULL NULL 3 
-
    -

    Description: -

    -

    Style reax computes the ReaxFF potential of van Duin, Goddard and -co-workers. ReaxFF uses distance-dependent bond-order functions to -represent the contributions of chemical bonding to the potential -energy. There is more than one version of ReaxFF. The version -implemented in LAMMPS uses the functional forms documented in the -supplemental information of the following paper: -(Chenoweth). The version integrated into LAMMPS matches -the most up-to-date version of ReaxFF as of summer 2010. -

    -

    WARNING: pair style reax is now deprecated and will soon be retired. Users -should switch to pair_style reax/c. The reax style -differs from the reax/c style in the lo-level implementation details. -The reax style is a -Fortran library, linked to LAMMPS. The reax/c style was initially -implemented as stand-alone C code and is now integrated into LAMMPS as -a package. -

    -

    LAMMPS requires that a file called ffield.reax be provided, containing -the ReaxFF parameters for each atom type, bond type, etc. The format -is identical to the ffield file used by van Duin and co-workers. The -filename is required as an argument in the pair_coeff command. Any -value other than "ffield.reax" will be rejected (see below). -

    -

    LAMMPS provides several different versions of ffield.reax in its -potentials dir, each called potentials/ffield.reax.label. These are -documented in potentials/README.reax. The default ffield.reax -contains parameterizations for the following elements: C, H, O, N, S. -

    -

    IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force -field files with LAMMPS. Adri van Duin's group at PSU is the central -repository for this kind of data as they are continuously deriving and -updating parameterizations for different classes of materials. You -can visit their WWW site at -http://www.engr.psu.edu/adri, register -as a "new user", and then submit a request to their group describing -material(s) you are interested in modeling with ReaxFF. They can tell -you what is currently available or what it would take to create a -suitable ReaxFF parameterization. -

    -

    The format of these files is identical to that used originally by van -Duin. We have tested the accuracy of pair_style reax potential -against the original ReaxFF code for the systems mentioned above. You -can use other ffield files for specific chemical systems that may be -available elsewhere (but note that their accuracy may not have been -tested). -

    -

    The hbcut, hbnewflag, tripflag, and precision settings are -optional arguments. If none are provided, default settings are used: -hbcut = 6 (which is Angstroms in real units), hbnewflag = 1 (use -new hbond function style), tripflag = 1 (apply stabilization to all -triple bonds), and precision = 1.0e-6 (one part in 10^6). If you -wish to override any of these defaults, then all of the settings must -be specified. -

    -

    Two examples using pair_style reax are provided in the examples/reax -sub-directory, along with corresponding examples for -pair_style reax/c. -

    -

    Use of this pair style requires that a charge be defined for every -atom since the reax pair style performs a charge equilibration (QEq) -calculation. See the atom_style and -read_data commands for details on how to specify -charges. -

    -

    The thermo variable evdwl stores the sum of all the ReaxFF potential -energy contributions, with the exception of the Coulombic and charge -equilibration contributions which are stored in the thermo variable -ecoul. The output of these quantities is controlled by the -thermo command. -

    -

    This pair style tallies a breakdown of the total ReaxFF potential -energy into sub-categories, which can be accessed via the compute -pair command as a vector of values of length 14. -The 14 values correspond to the following sub-categories (the variable -names in italics match those used in the ReaxFF FORTRAN library): -

    -
    1. eb = bond energy -
    2. ea = atom energy -
    3. elp = lone-pair energy -
    4. emol = molecule energy (always 0.0) -
    5. ev = valence angle energy -
    6. epen = double-bond valence angle penalty -
    7. ecoa = valence angle conjugation energy -
    8. ehb = hydrogen bond energy -
    9. et = torsion energy -
    10. eco = conjugation energy -
    11. ew = van der Waals energy -
    12. ep = Coulomb energy -
    13. efi = electric field energy (always 0.0) -
    14. eqeq = charge equilibration energy -
    -

    To print these quantities to the log file (with descriptive column -headings) the following commands could be included in an input script: -

    -
    compute reax all pair reax
-variable eb  	 equal c_reax[1]
-variable ea  	 equal c_reax[2] 
-...
-variable eqeq 	 equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq 
-
    -

    Only a single pair_coeff command is used with the reax style which -specifies a ReaxFF potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N indices = mapping of ReaxFF elements to atom types -
    -

    The specification of the filename and the mapping of LAMMPS atom types -recognized by the ReaxFF is done differently than for other LAMMPS -potentials, due to the non-portable difficulty of passing character -strings (e.g. filename, element names) between C++ and Fortran. -

    -

    The filename has to be "ffield.reax" and it has to exist in the -directory you are running LAMMPS in. This means you cannot prepend a -path to the file in the potentials dir. Rather, you should copy that -file into the directory you are running from. If you wish to use -another ReaxFF potential file, then name it "ffield.reax" and put it -in the directory you run from. -

    -

    In the ReaxFF potential file, near the top, after the general -parameters, is the atomic parameters section that contains element -names, each with a couple dozen numeric parameters. If there are M -elements specified in the ffield file, think of these as numbered 1 -to M. Each of the N indices you specify for the N atom types of LAMMPS -atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will -be mapped to whatever element you specify as the first index value, -etc. If a mapping value is specified as NULL, the mapping is not -performed. This can be used when a ReaxFF potential is used as part -of the hybrid pair style. The NULL values are placeholders for atom -types that will be used with other potentials. -

    -

    IMPORTANT NOTE: Currently the reax pair style cannot be used as part -of the hybrid pair style. Some additional changes still need to be -made to enable this. -

    -

    As an example, say your LAMMPS simulation has 4 atom types and the -elements are ordered as C, H, O, N in the ffield file. If you want -the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be -H, you would use the following pair_coeff command: -

    -
    pair_coeff * * ffield.reax 1 1 4 2 
-
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real units. You can use -the ReaxFF potential with any LAMMPS units, but you would need to -create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "real" units. -

    -

    Related commands: -

    -

    pair_coeff, pair_style reax/c, -fix_reax_bonds -

    -

    Default: -

    -

    The keyword defaults are hbcut = 6, hbnewflag = 1, tripflag = 1, -precision = 1.0e-6. -

    -
    - - - -

    (Chenoweth_2008) Chenoweth, van Duin and Goddard, -Journal of Physical Chemistry A, 112, 1040-1053 (2008). -

    - diff --git a/doc/doc2/pair_reax_c.html b/doc/doc2/pair_reax_c.html deleted file mode 100644 index 49e0e59e1a..0000000000 --- a/doc/doc2/pair_reax_c.html +++ /dev/null @@ -1,323 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style reax/c command -

    -

    Syntax: -

    -
    pair_style reax/c cfile keyword value 
-
    -
    • cfile = NULL or name of a control file - -
    • zero or more keyword/value pairs may be appended - -
      keyword = checkqeq or lgvdw or safezone or mincap
-  checkqeq value = yes or no = whether or not to require qeq/reax fix 
-  lgvdw value = yes or no = whether or not to use a low gradient vdW correction
-  safezone = factor used for array allocation
-  mincap = minimum size for array allocation 
-
      - -
    -

    Examples: -

    -
    pair_style reax/c NULL
-pair_style reax/c controlfile checkqeq no
-pair_style reax/c NULL lgvdw yes
-pair_style reax/c NULL safezone 1.6 mincap 100
-pair_coeff * * ffield.reax C H O N 
-
    -

    Description: -

    -

    Style reax/c computes the ReaxFF potential of van Duin, Goddard and -co-workers. ReaxFF uses distance-dependent bond-order functions to -represent the contributions of chemical bonding to the potential -energy. There is more than one version of ReaxFF. The version -implemented in LAMMPS uses the functional forms documented in the -supplemental information of the following paper: (Chenoweth et al., -2008). The version integrated into LAMMPS matches -the most up-to-date version of ReaxFF as of summer 2010. For more -technical details about the pair reax/c implementation of ReaxFF, see -the (Aktulga) paper. -

    -

    The reax/c style differs from the pair_style reax -command in the lo-level implementation details. The reax style is a -Fortran library, linked to LAMMPS. The reax/c style was initially -implemented as stand-alone C code and is now integrated into LAMMPS as -a package. -

    -

    LAMMPS provides several different versions of ffield.reax in its -potentials dir, each called potentials/ffield.reax.label. These are -documented in potentials/README.reax. The default ffield.reax -contains parameterizations for the following elements: C, H, O, N, S. -

    -

    The format of these files is identical to that used originally by van -Duin. We have tested the accuracy of pair_style reax/c potential -against the original ReaxFF code for the systems mentioned above. You -can use other ffield files for specific chemical systems that may be -available elsewhere (but note that their accuracy may not have been -tested). -

    -

    IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force -field files with LAMMPS. Adri van Duin's group at PSU is the central -repository for this kind of data as they are continuously deriving and -updating parameterizations for different classes of materials. You -can visit their WWW site at -http://www.engr.psu.edu/adri, register -as a "new user", and then submit a request to their group describing -material(s) you are interested in modeling with ReaxFF. They can tell -you what is currently available or what it would take to create a -suitable ReaxFF parameterization. -

    -

    The cfile setting can be specified as NULL, in which case default -settings are used. A control file can be specified which defines -values of control variables. Some control variables are -global parameters for the ReaxFF potential. Others define certain -performance and output settings. -Each line in the control file specifies the value for -a control variable. The format of the control file is described -below. -

    -

    IMPORTANT NOTE: The LAMMPS default values for the ReaxFF global parameters -correspond to those used by -Adri van Duin's stand-alone serial code. If these are changed by -setting control variables in the control file, the results from -LAMMPS and the serial code will not agree. -

    -

    Two examples using pair_style reax/c are provided in the examples/reax -sub-directory, along with corresponding examples for -pair_style reax. -

    -

    Use of this pair style requires that a charge be defined for every -atom. See the atom_style and -read_data commands for details on how to specify -charges. -

    -

    The ReaxFF parameter files provided were created using a charge -equilibration (QEq) model for handling the electrostatic interactions. -Therefore, by default, LAMMPS requires that the fix -qeq/reax command be used with pair_style reax/c -when simulating a ReaxFF model, to equilibrate charge each timestep. -Using the keyword checkqeq with the value no -turns off the check for fix qeq/reax, -allowing a simulation to be run without charge equilibration. -In this case, the static charges you -assign to each atom will be used for computing the electrostatic -interactions in the system. -See the fix qeq/reax command for details. -

    -

    Using the optional keyword lgvdw with the value yes turns on -the low-gradient correction of the ReaxFF/C for long-range -London Dispersion, as described in the (Liu) paper. Force field -file ffield.reax.lg is designed for this correction, and is trained -for several energetic materials (see "Liu"). When using lg-correction, -recommended value for parameter thb is 0.01, which can be set in the -control file. Note: Force field files are different for the original -or lg corrected pair styles, using wrong ffield file generates an error message. -

    -

    Optional keywords safezone and mincap are used for allocating -reax/c arrays. Increase these values can avoid memory problems, such -as segmentation faults and bondchk failed errors, that could occur under -certain conditions. -

    -

    The thermo variable evdwl stores the sum of all the ReaxFF potential -energy contributions, with the exception of the Coulombic and charge -equilibration contributions which are stored in the thermo variable -ecoul. The output of these quantities is controlled by the -thermo command. -

    -

    This pair style tallies a breakdown of the total ReaxFF potential -energy into sub-categories, which can be accessed via the compute -pair command as a vector of values of length 14. -The 14 values correspond to the following sub-categories (the variable -names in italics match those used in the original FORTRAN ReaxFF code): -

    -
    1. eb = bond energy -
    2. ea = atom energy -
    3. elp = lone-pair energy -
    4. emol = molecule energy (always 0.0) -
    5. ev = valence angle energy -
    6. epen = double-bond valence angle penalty -
    7. ecoa = valence angle conjugation energy -
    8. ehb = hydrogen bond energy -
    9. et = torsion energy -
    10. eco = conjugation energy -
    11. ew = van der Waals energy -
    12. ep = Coulomb energy -
    13. efi = electric field energy (always 0.0) -
    14. eqeq = charge equilibration energy -
    -

    To print these quantities to the log file (with descriptive column -headings) the following commands could be included in an input script: -

    -
    compute reax all pair reax/c
-variable eb  	 equal c_reax[1]
-variable ea  	 equal c_reax[2] 
-...
-variable eqeq 	 equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq 
-
    -

    Only a single pair_coeff command is used with the reax/c style which -specifies a ReaxFF potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N indices = ReaxFF elements -
    -

    The filename is the ReaxFF potential file. Unlike for the reax -pair style, any filename can be used. -

    -

    In the ReaxFF potential file, near the top, after the general -parameters, is the atomic parameters section that contains element -names, each with a couple dozen numeric parameters. If there are M -elements specified in the ffield file, think of these as numbered 1 -to M. Each of the N indices you specify for the N atom types of LAMMPS -atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will -be mapped to whatever element you specify as the first index value, -etc. If a mapping value is specified as NULL, the mapping is not -performed. This can be used when the reax/c style is used as part -of the hybrid pair style. The NULL values are placeholders for atom -types that will be used with other potentials. -

    -

    As an example, say your LAMMPS simulation has 4 atom types and the -elements are ordered as C, H, O, N in the ffield file. If you want -the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be -H, you would use the following pair_coeff command: -

    -
    pair_coeff * * ffield.reax C C N H 
-
    -
    - -

    The format of a line in the control file is as follows: -

    -
    variable_name value 
-
    -

    and it may be followed by an "!" character and a trailing comment. -

    -

    If the value of a control variable is not specified, then default -values are used. What follows is the list of variables along with a -brief description of their use and default values. -

    -

    simulation_name: Output files produced by pair_style reax/c carry -this name + extensions specific to their contents. Partial energies -are reported with a ".pot" extension, while the trajectory file has -".trj" extension. -

    -

    tabulate_long_range: To improve performance, long range interactions -can optionally be tabulated (0 means no tabulation). Value of this -variable denotes the size of the long range interaction table. The -range from 0 to long range cutoff (defined in the ffield file) is -divided into tabulate_long_range points. Then at the start of -simulation, we fill in the entries of the long range interaction table -by computing the energies and forces resulting from van der Waals and -Coulomb interactions between every possible atom type pairs present in -the input system. During the simulation we consult to the long range -interaction table to estimate the energy and forces between a pair of -atoms. Linear interpolation is used for estimation. (default value = -0) -

    -

    energy_update_freq: Denotes the frequency (in number of steps) of -writes into the partial energies file. (default value = 0) -

    -

    nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms) -regarding the bonded interactions. (default value = 5.0) -

    -

    hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen -bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen - bonds) -

    -

    bond_graph_cutoff: is the threshold used in determining what is a -physical bond, what is not. Bonds and angles reported in the -trajectory file rely on this cutoff. (default value = 0.3) -

    -

    thb_cutoff: cutoff value for the strength of bonds to be considered in -three body interactions. (default value = 0.001) -

    -

    thb_cutoff_sq: cutoff value for the strength of bond order products -to be considered in three body interactions. (default value = 0.00001) -

    -

    write_freq: Frequency of writes into the trajectory file. (default -value = 0) -

    -

    traj_title: Title of the trajectory - not the name of the trajectory -file. -

    -

    atom_info: 1 means print only atomic positions + charge (default = 0) -

    -

    atom_forces: 1 adds net forces to atom lines in the trajectory file -(default = 0) -

    -

    atom_velocities: 1 adds atomic velocities to atoms line (default = 0) -

    -

    bond_info: 1 prints bonds in the trajectory file (default = 0) -

    -

    angle_info: 1 prints angles in the trajectory file (default = 0) -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair style is part of the USER-REAXC package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real units. You can use -the ReaxFF potential with any LAMMPS units, but you would need to -create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "real" units. -

    -

    Related commands: -

    -

    pair_coeff, fix qeq/reax, fix -reax/c/bonds, fix -reax/c/species, pair_style -reax -

    -

    Default: -

    -

    The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2, -mincap = 50. -

    -
    - - - -

    (Chenoweth_2008) Chenoweth, van Duin and Goddard, -Journal of Physical Chemistry A, 112, 1040-1053 (2008). -

    - - -

    (Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, -245-259 (2012). -

    - - -

    (Liu) L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal -of Physical Chemistry A, 115, 11016-11022 (2011). -

    - diff --git a/doc/doc2/pair_resquared.html b/doc/doc2/pair_resquared.html deleted file mode 100644 index e391abdbc9..0000000000 --- a/doc/doc2/pair_resquared.html +++ /dev/null @@ -1,244 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style resquared command -

    -

    pair_style resquared/gpu command -

    -

    pair_style resquared/omp command -

    -

    Syntax: -

    -
    pair_style resquared cutoff 
-
    -
    • cutoff = global cutoff for interactions (distance units) -
    -

    Examples: -

    -
    pair_style resquared 10.0
-pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 
-
    -

    Description: -

    -

    Style resquared computes the RE-squared anisotropic interaction -(Everaers), (Babadi) between pairs of -ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal -interactions, the potential considers the ellipsoid as being comprised -of small spheres of size sigma. LJ particles are a single sphere of -size sigma. The distinction is made to allow the pair style to make -efficient calculations of ellipsoid/solvent interactions. -

    -

    Details for the equations used are given in the references below and -in this supplementary document. -

    -

    Use of this pair style requires the NVE, NVT, or NPT fixes with the -asphere extension (e.g. fix nve/asphere) in -order to integrate particle rotation. Additionally, atom_style -ellipsoid should be used since it defines the -rotational state and the size and shape of each ellipsoidal particle. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands: -

    -
    • A12 = Energy Prefactor/Hamaker constant (energy units) -
    • sigma = atomic interaction diameter (distance units) -
    • epsilon_i_a = relative well depth of type I for side-to-side interactions -
    • epsilon_i_b = relative well depth of type I for face-to-face interactions -
    • epsilon_i_c = relative well depth of type I for end-to-end interactions -
    • epsilon_j_a = relative well depth of type J for side-to-side interactions -
    • epsilon_j_b = relative well depth of type J for face-to-face interactions -
    • epsilon_j_c = relative well depth of type J for end-to-end interactions -
    • cutoff (distance units) -
    -

    The parameters used depend on the type of the interacting particles, -i.e. ellipsoids or LJ spheres. The type of a particle is determined -by the diameters specified for its 3 shape paramters. If all 3 shape -parameters = 0.0, then the particle is treated as an LJ sphere. The -epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If -the 3 shape paraemters are > 0.0, then the particle is treated as an -ellipsoid (even if the 3 parameters are equal to each other). -

    -

    A12 specifies the energy prefactor which depends on the types of the -two interacting particles. -

    -

    For ellipsoid/ellipsoid interactions, the interaction is computed by -the formulas in the supplementary docuement referenced above. A12 is -the Hamaker constant as described in (Everaers). In LJ -units: -

    -
    -
    -

    where rho gives the number density of the spherical particles -composing the ellipsoids and epsilon_LJ determines the interaction -strength of the spherical particles. -

    -

    For ellipsoid/LJ sphere interactions, the interaction is also computed -by the formulas in the supplementary docuement referenced above. A12 -has a modifed form (see here for -details): -

    -
    -
    -

    For ellipsoid/LJ sphere interactions, a correction to the distance- -of-closest approach equation has been implemented to reduce the error -from two particles of disparate sizes; see this supplementary -document. -

    -

    For LJ sphere/LJ sphere interactions, the interaction is computed -using the standard Lennard-Jones formula, which is much cheaper to -compute than the ellipsoidal formulas. A12 is used as epsilon in the -standard LJ formula: -

    -
    -
    -

    and the specified sigma is used as the sigma in the standard LJ -formula. -

    -

    When one of both of the interacting particles are ellipsoids, then -sigma specifies the diameter of the continuous distribution of -constituent particles within each ellipsoid used to model the -RE-squared potential. Note that this is a different meaning for -sigma than the pair_style gayberne potential -uses. -

    -

    The epsilon_i and epsilon_j coefficients are defined for atom types, -not for pairs of atom types. Thus, in a series of pair_coeff -commands, they only need to be specified once for each atom type. -

    -

    Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are -non-zero, the three values are assigned to atom type I. If all the -epsilon_i values are zero, they are ignored. If any of epsilon_j_a, -epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned -to atom type J. If all three epsilon_i values are zero, they are -ignored. Thus the typical way to define the epsilon_i and epsilon_j -coefficients is to list their values in "pair_coeff I J" commands when -I = J, but set them to 0.0 when I != J. If you do list them when I != -J, you should insure they are consistent with their values in other -pair_coeff commands. -

    -

    Note that if this potential is being used as a sub-style of -pair_style hybrid, and there is no "pair_coeff I I" -setting made for RE-squared for a particular type I (because I-I -interactions are computed by another hybrid pair potential), then you -still need to insure the epsilon a,b,c coefficients are assigned to -that type in a "pair_coeff I J" command. -

    -

    For large uniform molecules it has been shown that the epsilon_*_* -energy parameters are approximately representable in terms of local -contact curvatures (Everaers): -

    -
    -
    -

    where a, b, and c give the particle diameters. -

    -

    The last coefficient is optional. If not specified, the global cutoff -specified in the pair_style command is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance can be mixed, but only for sphere pairs. The -default mix value is geometric. See the "pair_modify" command for -details. Other type pairs cannot be mixed, due to the different -meanings of the energy prefactors used to calculate the interactions -and the implicit dependence of the ellipsoid-sphere interaction on the -equation for the Hamaker constant presented here. Mixing of sigma and -epsilon followed by calculation of the energy prefactors using the -equations above is recommended. -

    -

    This pair styles supports the pair_modify shift -option for the energy of the Lennard-Jones portion of the pair -interaction, but only for sphere-sphere interactions. There is no -shifting performed for ellipsoidal interactions due to the anisotropic -dependence of the interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords of the run_style -command. -

    -
    - -

    Restrictions: -

    -

    This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This pair style requires that atoms be ellipsoids as defined by the -atom_style ellipsoid command. -

    -

    Particles acted on by the potential can be finite-size aspherical or -spherical particles, or point particles. Spherical particles have all -3 of their shape parameters equal to each other. Point particles have -all 3 of their shape parameters equal to 0.0. -

    -

    The distance-of-closest-approach approximation used by LAMMPS becomes -less accurate when high-aspect ratio ellipsoids are used. -

    -

    Related commands: -

    -

    pair_coeff, fix nve/asphere, -compute temp/asphere, pair_style -gayberne -

    -

    Default: none -

    -
    - - - -

    (Everaers) Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). -

    - - -

    (Berardi) Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). -

    - diff --git a/doc/doc2/pair_sdk.html b/doc/doc2/pair_sdk.html deleted file mode 100644 index edfb1d2202..0000000000 --- a/doc/doc2/pair_sdk.html +++ /dev/null @@ -1,169 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style lj/sdk command -

    -

    pair_style lj/sdk/gpu command -

    -

    pair_style lj/sdk/kk command -

    -

    pair_style lj/sdk/omp command -

    -

    pair_style lj/sdk/coul/long command -

    -

    pair_style lj/sdk/coul/long/gpu command -

    -

    pair_style lj/sdk/coul/long/omp command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = lj/sdk or lj/sdk/coul/long -
    • args = list of arguments for a particular style -
    -
      lj/sdk args = cutoff
-    cutoff = global cutoff for Lennard Jones interactions (distance units)
-  lj/sdk/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
-
    -

    Examples: -

    -
    pair_style lj/sdk 2.5
-pair_coeff 1 1 lj12_6 1 1.1 2.8 
-
    -
    pair_style lj/sdk/coul/long 10.0
-pair_style lj/sdk/coul/long 10.0 12.0
-pair_coeff 1 1 lj9_6 100.0 3.5 12.0 
-
    -

    Description: -

    -

    The lj/sdk styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, -given by -

    -
    -
    -

    as required for the SDK Coarse-grained MD parametrization discussed in -(Shinoda) and (DeVane). Rc is the cutoff. -

    -

    Style lj/sdk/coul/long computes the adds Coulombic interactions -with an additional damping factor applied so it can be used in -conjunction with the kspace_style command and -its ewald or pppm or pppm/cg option. The Coulombic cutoff -specified for this style means that pairwise interactions within -this distance are computed directly; interactions outside that -distance are computed in reciprocal space. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • cg_type (lj9_6, lj12_4, or lj12_6) -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff1 (distance units) -
    -

    Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum. The prefactors -are chosen so that the potential minimum is at -epsilon. -

    -

    The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. -

    -

    For lj/sdk/coul/long only the LJ cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP, and OPT packages respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, and rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/sdk pair styles cannot be mixed, -since different pairs may have different exponents. So all parameters -for all pairs have to be specified explicitly through the "pair_coeff" -command. Defining then in a data file is also not supported, due to -limitations of that file format. -

    -

    All of the lj/sdk pair styles support the -pair_modify shift option for the energy of the -Lennard-Jones portion of the pair interaction. -

    -

    The lj/sdk/coul/long pair styles support the -pair_modify table option since they can tabulate -the short-range portion of the long-range Coulombic interaction. -

    -

    All of the lj/sdk pair styles write their information to binary -restart files, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. -

    -

    The lj/sdk and lj/cut/coul/long pair styles do not support -the use of the inner, middle, and outer keywords of the run_style -respa command. -

    -
    - -

    Restrictions: -

    -

    All of the lj/sdk pair styles are part of the USER-CG-CMM package. -The lj/sdk/coul/long style also requires the KSPACE package to be -built (which is enabled by default). They are only enabled if LAMMPS -was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, angle_style sdk -

    -

    Default: none -

    -
    - - - -

    (Shinoda) Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). -

    - - -

    (DeVane) Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008). -

    - diff --git a/doc/doc2/pair_smd_hertz.html b/doc/doc2/pair_smd_hertz.html deleted file mode 100644 index 8a7f29107c..0000000000 --- a/doc/doc2/pair_smd_hertz.html +++ /dev/null @@ -1,60 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style smd/hertz command -

    -

    Syntax: -

    -
    pair_style smd/hertz scale_factor 
-
    -

    Examples: -

    -

    pair_style smd/hertz 1.0 -pair_coeff 1 1 -

    -

    Description: -

    -

    The smd/hertz style calculates contact forces between SPH particles belonging to different physical bodies. -

    -

    The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles -(whose spatial extents are defined via its contact radius). -The effect is that a particles cannot penetrate into each other. -The parameter has units of pressure and should equal roughly one half -of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles. -

    -

    The parameter scale_factor can be used to scale the particles' contact radii. This can be useful to control how close -particles can approach each other. Usually, scale_factor=1.0. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. -

    -
    - -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - diff --git a/doc/doc2/pair_smd_tlsph.html b/doc/doc2/pair_smd_tlsph.html deleted file mode 100644 index 17b556c6a7..0000000000 --- a/doc/doc2/pair_smd_tlsph.html +++ /dev/null @@ -1,70 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style smd/tlsph command -

    -

    Syntax: -

    -
    pair_style smd/tlsph args 
-
    -

    Examples: -

    -

    pair_style smd/tlsph -

    -

    Description: -

    -

    The smd/tlsph style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm. -

    -

    This pair style is invoked with the following command: -

    -
    pair_style smd/tlsph
-pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
-               *END 
-
    -

    Here, i and j denote the LAMMPS particle types for which this pair style is -defined. Note that i and j must be equal, i.e., no tlsph cross interactions -between different particle types are allowed. -In contrast to the usual LAMMPS pair coeff definitions, which are given solely a -number of floats and integers, the tlsph pair coeff definition is organised using -keywords. These keywords mark the beginning of different sets of parameters for particle properties, -material constitutive models, and damage models. The pair coeff line must be terminated with -the *END keyword. The use the line continuation operator & is recommended. A typical -invocation of the tlsph for a solid body would consist of an equation of state for computing -the pressure (the diagonal components of the stress tensor), and a material model to compute shear -stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added. -

    -

    Please see the SMD user guide for a complete listing of the possible keywords and material models. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. -

    -
    - -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - diff --git a/doc/doc2/pair_smd_triangulated_surface.html b/doc/doc2/pair_smd_triangulated_surface.html deleted file mode 100644 index 93d49818bc..0000000000 --- a/doc/doc2/pair_smd_triangulated_surface.html +++ /dev/null @@ -1,61 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style smd/tri_surface command -

    -

    Syntax: -

    -
    pair_style smd/tri_surface scale_factor 
-
    -

    Examples: -

    -

    pair_style smd/tri_surface 1.0 -pair_coeff 1 1 -

    -

    Description: -

    -

    The smd/tri_surface style calculates contact forces between SPH particles and a rigid wall boundary defined via the -smd/wall_surface fix. -

    -

    The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle -(whose spatial extents are defined via its contact radius) and the triangle. -The effect is that a particle cannot penetrate into the triangular surface. -The parameter has units of pressure and should equal roughly one half -of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle -

    -

    The parameter scale_factor can be used to scale the particles' contact radii. This can be useful to control how close -particles can approach the triangulated surface. Usually, scale_factor=1.0. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. -

    -
    - -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - diff --git a/doc/doc2/pair_smd_ulsph.html b/doc/doc2/pair_smd_ulsph.html deleted file mode 100644 index 301f5073da..0000000000 --- a/doc/doc2/pair_smd_ulsph.html +++ /dev/null @@ -1,76 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style smd/ulsph command -

    -

    Syntax: -

    -
    pair_style smd/ulsph args 
-
    -
  • these keywords must be given - -

    keyword = *DENSITY_SUMMATION or *DENSITY_CONTINUITY and *VELOCITY_GRADIENT or *NO_VELOCITY_GRADIENT and *GRADIENT_CORRECTION or *NO_GRADIENT_CORRECTION -

    -

    Examples: -

    -

    pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION -

    -

    Description: -

    -

    The smd/ulsph style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm. -

    -

    This pair style is invoked similar to the following command: -

    -
    pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
-pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
-               *END 
-
    -

    Here, i and j denote the LAMMPS particle types for which this pair style is -defined. Note that i and j can be different, i.e., ulsph cross interactions -between different particle types are allowed. However, i--i respectively j--j pair_coeff lines have to preceed a cross interaction. -In contrast to the usual LAMMPS pair coeff definitions, which are given solely a -number of floats and integers, the ulsph pair coeff definition is organised using -keywords. These keywords mark the beginning of different sets of parameters for particle properties, -material constitutive models, and damage models. The pair coeff line must be terminated with -the *END keyword. The use the line continuation operator & is recommended. A typical -invocation of the ulsph for a solid body would consist of an equation of state for computing -the pressure (the diagonal components of the stress tensor), and a material model to compute shear -stresses (the off-diagonal components of the stress tensor). -

    -

    Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended. -

    -

    Please see the SMD user guide for a complete listing of the possible keywords and material models. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. -

    -
    - -

    Restrictions: -

    -

    This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - diff --git a/doc/doc2/pair_smtbq.html b/doc/doc2/pair_smtbq.html deleted file mode 100644 index 3efce316c9..0000000000 --- a/doc/doc2/pair_smtbq.html +++ /dev/null @@ -1,272 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style smtbq command -

    -

    Syntax: -

    -
    pair_style smtbq 
-
    -

    Examples: -

    -
    pair_style smtbq
-pair_coeff * * ffield.smtbq.Al2O3 O Al 
-
    -

    Description: -

    -

    This pair stylecomputes a variable charge SMTB-Q (Second-Moment -tight-Binding QEq) potential as described in SMTB-Q_1 and -SMTB-Q_2. Briefly, the energy of metallic-oxygen systems -is given by three contributions: -

    -
    -
    -

    where Etot is the total potential energy of the system, -EES is the electrostatic part of the total energy, -EOO is the interaction between oxygens and -EMO is a short-range interaction between metal and oxygen -atoms. This interactions depend on interatomic distance -rij and/or the charge Qi of atoms -i. Cut-off function enables smooth convergence to zero interaction. -

    -

    The parameters appearing in the upper expressions are set in the -ffield.SMTBQ.Syst file where Syst corresponds to the selected system -(e.g. field.SMTBQ.Al2O3). Exemples for TiO2, -Al2O3 are provided. A single pair_coeff command -is used with the SMTBQ styles which provides the path to the potential -file with parameters for needed elements. These are mapped to LAMMPS -atom types by specifying additional arguments after the potential -filename in the pair_coeff command. Note that atom type 1 must always -correspond to oxygen atoms. As an example, to simulate a TiO2 system, -atom type 1 has to be oxygen and atom type 2 Ti. The following -pair_coeff command should then be used: -

    -
    pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti 
-
    -The electrostatic part of the energy consists of two components - -

    self-energy of atom i in the form of a second order charge dependent -polynomial and a long-range Coulombic electrostatic interaction. The -latter uses the wolf summation method described in Wolf, -spherically truncated at a longer cutoff, Rcoul. The -charge of each ion is modeled by an orbital Slater which depends on -the principal quantum number (n) of the outer orbital shared by the -ion. -

    -

    Interaction between oxygen, EOO, consists of two parts, -an attractive and a repulsive part. The attractive part is effective -only at short range (< r2OO). The attractive -contribution was optimized to study surfaces reconstruction -(e.g. SMTB-Q_2 in TiO2) and is not necessary -for oxide bulk modeling. The repulsive part is the Pauli interaction -between the electron clouds of oxygen. The Pauli repulsion and the -coulombic electrostatic interaction have same cut off value. In the -ffield.SMTBQ.Syst, the keyword 'buck' allows to consider only the -repulsive O-O interactions. The keyword 'buckPlusAttr' allows to -consider the repulsive and the attractive O-O interactions. -

    -

    The short-range interaction between metal-oxygen, EMO is -based on the second moment approximation of the density of states with -a N-body potential for the band energy term, -Eicov, and a Born-Mayer type repulsive terms -as indicated by the keyword 'second_moment' in the -ffield.SMTBQ.Syst. The energy band term is given by: -

    -
    -
    -

    where ηi is the stoichiometry of atom i, -δQi is the charge delocalization of atom i, -compared to its formal charge -QFi. n0, the number of hybridized -orbitals, is calculated with to the atomic orbitals shared -di and the stoichiometry -ηi. rc1 and rc2 are the two -cutoff radius around the fourth neighbors in the cutoff function. -

    -

    In the formalism used here, ξ0 is the energy -parameter. ξ0 is in tight-binding approximation the -hopping integral between the hybridized orbitals of the cation and the -anion. In the literature we find many ways to write the hopping -integral depending on whether one takes the point of view of the anion -or cation. These are equivalent vision. The correspondence between the -two visions is explained in appendix A of the article in the -SrTiO3 SMTB-Q_3 (parameter β shown in -this article is in fact the βO). To summarize the -relationship between the hopping integral ξ0 and the -others, we have in an oxide CnOm the following -relationship: -

    -
    -
    -

    Thus parameter μ, indicated above, is given by : μ = (√n -+ √m) ⁄ 2 -

    -

    The potential offers the possibility to consider the polarizability of -the electron clouds of oxygen by changing the slater radius of the -charge density around the oxygens through the parameters rBB, rB and -rS in the ffield.SMTBQ.Syst. This change in radius is performed -according to the method developed by E. Maras -SMTB-Q_2. This method needs to determine the number of -nearest neighbors around the oxygen. This calculation is based on -first (r1n) and second (r2n) distances -neighbors. -

    -

    The SMTB-Q potential is a variable charge potential. The equilibrium -charge on each atom is calculated by the electronegativity -equalization (QEq) method. See Rick for further detail. One -can adjust the frequency, the maximum number of iterative loop and the -convergence of the equilibrium charge calculation. To obtain the -energy conservation in NVE thermodynamic ensemble, we recommend to use -a convergence parameter in the interval 10-5 - -10-6 eV. -

    -

    The ffield.SMTBQ.Syst files are provided for few systems. They consist -of nine parts and the lines beginning with '#' are comments (note that -the number of comment lines matter). The first sections are on the -potential parameters and others are on the simulation options and -might be modified. Keywords are character type and must be enclosed in -quotation marks (''). -

    -

    1) Number of different element in the oxide: -

    -
    • Nelem= 2 or 3 -
    • Divided line -
    -

    2) Atomic parameters -

    -For the anion (oxygen) - -
    • Name of element (char) and stoichiometry in oxide -
    • Formal charge and mass of element -
    • Principal quantic number of outer orbital (n), electronegativity (χ0i) and hardness (J0i) -
    • Ionic radius parameters : max coordination number (coordBB = 6 by default), bulk coordination number (coordB), surface coordination number (coordS) and rBB, rB and rS the slater radius for each coordination number. (note : If you don't want to change the slater radius, use three identical radius values) -
    • Number of orbital shared by the element in the oxide (di) -
    • Divided line -
    -

    For each cations (metal): -

    -
    • Name of element (char) and stoichiometry in oxide -
    • Formal charge and mass of element -
    • Number of electron in outer orbital (ne), electronegativity (χ0i), hardness (J0i) and rSalter the slater radius for the cation. -
    • Number of orbitals shared by the elements in the oxide (di) -
    • Divided line -
    -

    3) Potential parameters: -

    -
    • Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively. -
    • Potential parameter: 

      	If type of potential is 'second_moment' : A (eV), p, ξ0 (eV) and q 
      						  rc1 (Å), rc2 (Å) and r0 (Å) 
       	If type of potential is 'buck' : C (eV) and ρ (Å) 
      	If type of potential is 'buckPlusAttr' : C (eV) and ρ (Å) 
      						 D (eV), B (Å-1), r1OO (Å) and r2OO (Å)
      -
    • Divided line -
    -

    4) Tables parameters: -

    -
    • Cutoff radius for the Coulomb interaction (Rcoul) -
    • Starting radius (rmin = 1,18845 Å) and increments (dr = 0,001 Å) for creating the potential table. -
    • Divided line -
    -

    5) Rick model parameter: -

    -
    • Nevery : parameter to set the frequency (1/Nevery) of the charge resolution. The charges are evaluated each Nevery time steps. -
    • Max number of iterative loop (loopmax) and precision criterion (prec) in eV of the charge resolution -
    • Divided line -
    -

    6) Coordination parameter: -

    -
    • First (r1n) and second (r2n) neighbor distances in Å -
    • Divided line -
    -

    7) Charge initialization mode: -

    -
    • Keyword (QInitMode) and initial oxygen charge (Qinit). If keyword = 'true', all oxygen charges are initially set equal to Qinit. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using read_data command. -
    • Divided line -
    -8) Mode for the electronegativity equalization (Qeq) - -
    • Keyword mode: 
       
      		QEqAll  (one QEq group)			|   no parameters 
      		QEqAllParallel (several QEq groups)	|   no parameters 
      		Surface			|   zlim   (QEq only for z>zlim)
      -
    • Parameter if necessary -
    • Divided line -
    -9) Verbose - -
    • If you want the code to work in verbose mode or not : 'true' or 'false' -
    • If you want to print or not in file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and NEnergy. This option writes in file every NEnergy time step. If the value is 'false' then NEnergy = 0. The file take into account the possibility to have several QEq group g then it writes: time step, number of atoms in group g, electrostatic part of energy, EES, the interaction between oxygen, EOO, and short range metal-oxygen interaction, EMO. -
    • If you want to print in file 'Electroneg_component.txt' the electronegativity component (∂Etot ⁄∂Qi) or not: 'true' or 'false' and NElectroneg.This option writes in file every NElectroneg time step. If the value is 'false' then NElectroneg = 0. The file consist in atom number i, atom type (1 for oxygen and # higher than 1 for metal), atom position: x, y and z, atomic charge of atom i, electrostatic part of atom i electronegativity, covalent part of atom i electronegativity, the hopping integral of atom i (Zβ2)i and box electronegativity. -
    -

    IMPORTANT NOTE: This last option slows down the calculation -dramatically. Use only with a single processor simulation. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -mix, shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -needs to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restriction: -

    -

    This pair style is part of the USER-SMTBQ package and is only enabled -if LAMMPS is built with that package. See the Making -LAMMPS section for more info. -

    -

    This potential requires using atom type 1 for oxygen and atom type -higher than 1 for metal atoms. -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    The SMTB-Q potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal units. -

    -
    - -

    Citing this work: -

    -

    Please cite related publication: N. Salles, O. Politano, E. Amzallag -and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 -

    -
    - - - -

    (SMTB-Q_1) N. Salles, O. Politano, E. Amzallag, R. Tetot, -Comput. Mater. Sci. 111 (2016) 181-189 -

    - - -

    (SMTB-Q_2) E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, -H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399 -

    - - -

    (SMTB-Q_3) R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface -Science 616, 19-8722 28 (2013) -

    - - -

    (Wolf) D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem -Phys, 110, 8254 (1999). -

    - - -

    (Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 -(1994). -

    - diff --git a/doc/doc2/pair_snap.html b/doc/doc2/pair_snap.html deleted file mode 100644 index c5fb036e4e..0000000000 --- a/doc/doc2/pair_snap.html +++ /dev/null @@ -1,201 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style snap command -

    -

    Syntax: -

    -
    pair_style snap 
-
    -

    Examples: -

    -
    pair_style snap
-pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P 
-
    -

    Description: -

    -

    Style snap computes interactions -using the spectral neighbor analysis potential (SNAP) -(Thompson). Like the GAP framework of Bartok et al. -(Bartok2010), (Bartok2013) -it uses bispectrum components -to characterize the local neighborhood of each atom -in a very general way. The mathematical definition of the -bispectrum calculation used by SNAP is identical -to that used of compute sna/atom. -In SNAP, the total energy is decomposed into a sum over -atom energies. The energy of atom i is -expressed as a weighted sum over bispectrum components. -

    -
    -
    -

    where B_k^i is the k-th bispectrum component of atom i, -and beta_k^alpha_i is the corresponding linear coefficient -that depends on alpha_i, the SNAP element of atom i. The -number of bispectrum components used and their definitions -depend on the values of twojmax and diagonalstyle -defined in the SNAP parameter file described below. -The bispectrum calculation is described in more detail -in compute sna/atom. -

    -

    Note that unlike for other potentials, cutoffs for SNAP potentials are -not set in the pair_style or pair_coeff command; they are specified in -the SNAP potential files themselves. -

    -

    Only a single pair_coeff command is used with the snap style which -specifies two SNAP files and the list SNAP element(s) to be -extracted. -The SNAP elements are mapped to LAMMPS atom types by specifying -N additional arguments after the 2nd filename in the pair_coeff -command, where N is the number of LAMMPS atom types: -

    -
    • SNAP element file -
    • Elem1, Elem2, ... -
    • SNAP parameter file -
    • N element names = mapping of SNAP elements to atom types -
    -

    As an example, if a LAMMPS indium phosphide simulation has 4 atoms -types, with the first two being indium and the 3rd and 4th being -phophorous, the pair_coeff command would look like this: -

    -
    pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The two filenames are for the element and parameter files, respectively. -The 'In' and 'P' arguments (between the file names) are the two elements -which will be extracted from the element file. The -two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the -SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types -3 and 4 to the SNAP 'P' element. -

    -

    If a SNAP mapping value is -specified as NULL, the mapping is not performed. -This can be used when a snap potential is used as part of the -hybrid pair style. The NULL values are placeholders for atom types -that will be used with other potentials. -

    -

    The name of the SNAP element file usually ends in the -".snapcoeff" extension. It may contain coefficients -for many SNAP elements. -Only those elements listed in the pair_coeff command are extracted. -The name of the SNAP parameter file usually ends in the ".snapparam" -extension. It contains a small number -of parameters that define the overall form of the SNAP potential. -See the pair_coeff doc page for alternate ways -to specify the path for these files. -

    -

    Quite commonly, -SNAP potentials are combined with one or more other LAMMPS pair styles -using the hybrid/overlay pair style. As an example, the SNAP -tantalum potential provided in the LAMMPS potentials directory -combines the snap and zbl pair styles. It is invoked -by the following commands: -

    -
    	variable zblcutinner equal 4
-	variable zblcutouter equal 4.8
-	variable zblz equal 73
-	pair_style hybrid/overlay &
-	zbl ${zblcutinner} ${zblcutouter} snap
-	pair_coeff * * zbl 0.0 
-	pair_coeff 1 1 zbl ${zblz}
-	pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
-	../potentials/Ta06A.snapparam Ta 
-
    -

    It is convenient to keep these commands in a separate file that can -be inserted in any LAMMPS input script using the include -command. -

    -

    The top of the SNAP element file can contain any number of blank and comment -lines (start with #), but follows a strict -format after that. The first non-blank non-comment -line must contain two integers: -

    -
    • nelem = Number of elements -
    • ncoeff = Number of coefficients -
    -

    This is followed by one block for each of the nelem elements. -The first line of each block contains three entries: -

    -
    • Element symbol (text string) -
    • R = Element radius (distance units) -
    • w = Element weight (dimensionless) -
    -

    This line is followed by ncoeff coefficients, one per line. -

    -

    The SNAP parameter file can contain blank and comment lines (start -with #) anywhere. Each non-blank non-comment line must contain one -keyword/value pair. The required keywords are rcutfac and -twojmax. Optional keywords are rfac0, rmin0, diagonalstyle, -and switchflag. -

    -

    The default values for these keywords are -

    -
    • rfac0 = 0.99363 -
    • rmin0 = 0.0 -
    • diagonalstyle = 3 -
    • switchflag = 0 -
    -

    Detailed definitions of these keywords are given on the compute -sna/atom doc page. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS with -user-specifiable parameters as described above. You never need to -specify a pair_coeff command with I != J arguments for this style. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the SNAP package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    compute sna/atom, -compute snad/atom, -compute snav/atom -

    -

    Default: none -

    -
    - - - -

    (Thompson) Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint -available at arXiv:1409.3880 -

    - - -

    (Bartok2010) Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). -

    - - -

    (Bartok2013) Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013). -

    - diff --git a/doc/doc2/pair_soft.html b/doc/doc2/pair_soft.html deleted file mode 100644 index e99ddacd65..0000000000 --- a/doc/doc2/pair_soft.html +++ /dev/null @@ -1,143 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style soft command -

    -

    pair_style soft/gpu command -

    -

    pair_style soft/omp command -

    -

    Syntax: -

    -
    pair_style soft cutoff 
-
    -
    • cutoff = global cutoff for soft interactions (distance units) -
    -

    Examples: -

    -
    pair_style soft 2.5
-pair_coeff * * 10.0
-pair_coeff 1 1 10.0 3.0 
-
    -
    pair_style soft 2.5
-pair_coeff * * 0.0
-variable prefactor equal ramp(0,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor 
-
    -

    Description: -

    -

    Style soft computes pairwise interactions with the formula -

    -
    -
    -

    It is useful for pushing apart overlapping atoms, since it does not -blow up as r goes to 0. A is a pre-factor that can be made to vary in -time from the start to the end of the run (see discussion below), -e.g. to start with a very soft potential and slowly harden the -interactions over time. Rc is the cutoff. See the fix -nve/limit command for another way to push apart -overlapping atoms. -

    -

    The following coefficients must be defined for each pair of atom types -via the pair_coeff command as in the examples above, -or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • A (energy units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global soft -cutoff is used. -

    -

    IMPORTANT NOTE: The syntax for pair_coeff with a -single A coeff is different in the current version of LAMMPS than in -older versions which took two values, Astart and Astop, to ramp -between them. This functionality is now available in a more general -form through the fix adapt command, as explained -below. Note that if you use an old input script and specify Astart -and Astop without a cutoff, then LAMMPS will interpret that as A and a -cutoff, which is probabably not what you want. -

    -

    The fix adapt command can be used to vary A for one -or more pair types over the course of a simulation, in which case -pair_coeff settings for A must still be specified, but will be -overridden. For example these commands will vary the prefactor A for -all pairwise interactions from 0.0 at the beginning to 30.0 at the end -of a run: -

    -
    variable prefactor equal ramp(0,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor 
-
    -

    Note that a formula defined by an equal-style variable -can use the current timestep, elapsed time in the current run, elapsed -time since the beginning of a series of runs, as well as access other -variables. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the A coefficient and cutoff -distance for this pair style can be mixed. A is always mixed via a -geometric rule. The cutoff is mixed according to the pair_modify -mix value. The default mix value is geometric. See the -"pair_modify" command for details. -

    -

    This pair style does not support the pair_modify -shift option, since the pair interaction goes to 0.0 at the cutoff. -

    -

    The pair_modify table and tail options are not -relevant for this pair style. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff, fix nve/limit, fix -adapt -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_sph_heatconduction.html b/doc/doc2/pair_sph_heatconduction.html deleted file mode 100644 index 570a324b87..0000000000 --- a/doc/doc2/pair_sph_heatconduction.html +++ /dev/null @@ -1,68 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style sph/heatconduction command -

    -

    Syntax: -

    -
    pair_style sph/heatconduction 
-
    -

    Examples: -

    -
    pair_style sph/heatconduction
-pair_coeff * * 1.0 2.4 
-
    -

    Description: -

    -

    The sph/heatconduction style computes heat transport between SPH particles. -The transport model is the diffusion euqation for the internal energy. -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above. -

    -
    • D diffusion coefficient (length^2/time units) -
    • h kernel function cutoff (distance units) -
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This style does not support the pair_modify -shift, table, and tail options. -

    -

    This style does not write information to binary restart -files. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. -

    -

    This style can only be used via the pair keyword of the run_style -respa command. It does not support the inner, -middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_sph/rhosum -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_sph_idealgas.html b/doc/doc2/pair_sph_idealgas.html deleted file mode 100644 index 4d45b2959c..0000000000 --- a/doc/doc2/pair_sph_idealgas.html +++ /dev/null @@ -1,82 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style sph/idealgas command -

    -

    Syntax: -

    -
    pair_style sph/idealgas 
-
    -

    Examples: -

    -
    pair_style sph/idealgas
-pair_coeff * * 1.0 2.4 
-
    -

    Description: -

    -

    The sph/idealgas style computes pressure forces between particles -according to the ideal gas equation of state: -

    -
    -
    -

    where gamma = 1.4 is the heat capacity ratio, rho is the local -density, and e is the internal energy per unit mass. This pair style -also computes Monaghan's artificial viscosity to prevent particles -from interpentrating (Monaghan). -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above. -

    -
    • nu artificial viscosity (no units) -
    • h kernel function cutoff (distance units) -
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This style does not support the pair_modify -shift, table, and tail options. -

    -

    This style does not write information to binary restart -files. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. -

    -

    This style can only be used via the pair keyword of the run_style -respa command. It does not support the inner, -middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_sph/rhosum -

    -

    Default: none -

    -
    - - - -

    (Monaghan) Monaghan and Gingold, Journal of Computational Physics, -52, 374-389 (1983). -

    - diff --git a/doc/doc2/pair_sph_lj.html b/doc/doc2/pair_sph_lj.html deleted file mode 100644 index 60cbdc67c8..0000000000 --- a/doc/doc2/pair_sph_lj.html +++ /dev/null @@ -1,86 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style sph/lj command -

    -

    Syntax: -

    -
    pair_style sph/lj 
-
    -

    Examples: -

    -
    pair_style sph/lj
-pair_coeff * * 1.0 2.4 
-
    -

    Description: -

    -

    The sph/lj style computes pressure forces between particles according -to the Lennard-Jones equation of state, which is computed according to -Ree's 1980 polynomial fit (Ree). The Lennard-Jones parameters -epsilon and sigma are set to unity. This pair style also computes -Monaghan's artificial viscosity to prevent particles from -interpentrating (Monaghan). -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above. -

    -
    • nu artificial viscosity (no units) -
    • h kernel function cutoff (distance units) -
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This style does not support the pair_modify -shift, table, and tail options. -

    -

    This style does not write information to binary restart -files. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. -

    -

    This style can only be used via the pair keyword of the run_style -respa command. It does not support the inner, -middle, outer keywords. -

    -

    Restrictions: -

    -

    As noted above, the Lennard-Jones parameters epsilon and sigma are set -to unity. -

    -

    This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_sph/rhosum -

    -

    Default: none -

    -
    - - - -

    (Ree) Ree, Journal of Chemical Physics, 73, 5401 (1980). -

    - - -

    (Monaghan) Monaghan and Gingold, Journal of Computational Physics, -52, 374-389 (1983). -

    - diff --git a/doc/doc2/pair_sph_rhosum.html b/doc/doc2/pair_sph_rhosum.html deleted file mode 100644 index 7e3f38a91a..0000000000 --- a/doc/doc2/pair_sph_rhosum.html +++ /dev/null @@ -1,69 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style sph/rhosum command -

    -

    Syntax: -

    -
    pair_style sph/rhosum Nstep 
-
    -
    • Nstep = timestep interval -
    -

    Examples: -

    -
    pair_style sph/rhosum 10
-pair_coeff * * 2.4 
-
    -

    Description: -

    -

    The sph/rhosum style computes the local particle mass density rho for -SPH particles by kernel function interpolation, every Nstep timesteps. -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above. -

    -
    • h (distance units) -
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This style does not support the pair_modify -shift, table, and tail options. -

    -

    This style does not write information to binary restart -files. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. -

    -

    This style can only be used via the pair keyword of the run_style -respa command. It does not support the inner, -middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_sph/taitwater -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_sph_taitwater.html b/doc/doc2/pair_sph_taitwater.html deleted file mode 100644 index 7c350f2f37..0000000000 --- a/doc/doc2/pair_sph_taitwater.html +++ /dev/null @@ -1,85 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style sph/taitwater command -

    -

    Syntax: -

    -
    pair_style sph/taitwater 
-
    -

    Examples: -

    -
    pair_style sph/taitwater
-pair_coeff * * 1000.0 1430.0 1.0 2.4 
-
    -

    Description: -

    -

    The sph/taitwater style computes pressure forces between SPH particles -according to Tait's equation of state: -

    -
    -
    -

    where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the -reference density and c_0 the reference speed of sound. -

    -

    This pair style also computes Monaghan's artificial viscosity to -prevent particles from interpentrating (Monaghan). -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above. -

    -
    • rho0 reference density (mass/volume units) -
    • c0 reference soundspeed (distance/time units) -
    • nu artificial viscosity (no units) -
    • h kernel function cutoff (distance units) -
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This style does not support the pair_modify -shift, table, and tail options. -

    -

    This style does not write information to binary restart -files. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. -

    -

    This style can only be used via the pair keyword of the run_style -respa command. It does not support the inner, -middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_sph/rhosum -

    -

    Default: none -

    -
    - - - -

    (Monaghan) Monaghan and Gingold, Journal of Computational Physics, -52, 374-389 (1983). -

    - diff --git a/doc/doc2/pair_sph_taitwater_morris.html b/doc/doc2/pair_sph_taitwater_morris.html deleted file mode 100644 index 4a2568ff79..0000000000 --- a/doc/doc2/pair_sph_taitwater_morris.html +++ /dev/null @@ -1,83 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style sph/taitwater/morris command -

    -

    Syntax: -

    -
    pair_style sph/taitwater/morris 
-
    -

    Examples: -

    -
    pair_style sph/taitwater/morris
-pair_coeff * * 1000.0 1430.0 1.0 2.4 
-
    -

    Description: -

    -

    The sph/taitwater/morris style computes pressure forces between SPH -particles according to Tait's equation of state: -

    -
    -
    -

    where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the -reference density and c_0 the reference speed of sound. -

    -

    This pair style also computes laminar viscosity (Morris). -

    -

    See this PDF guide to using SPH in -LAMMPS. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above. -

    -
    • rho0 reference density (mass/volume units) -
    • c0 reference soundspeed (distance/time units) -
    • nu dynamic viscosity (mass*distance/time units) -
    • h kernel function cutoff (distance units) -
    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    This style does not support the pair_modify -shift, table, and tail options. -

    -

    This style does not write information to binary restart -files. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. -

    -

    This style can only be used via the pair keyword of the run_style -respa command. It does not support the inner, -middle, outer keywords. -

    -

    Restrictions: -

    -

    This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Related commands: -

    -

    pair_coeff, pair_sph/rhosum -

    -

    Default: none -

    -
    - - - -

    (Morris) Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997). -

    - diff --git a/doc/doc2/pair_srp.html b/doc/doc2/pair_srp.html deleted file mode 100644 index 173a2f55ba..0000000000 --- a/doc/doc2/pair_srp.html +++ /dev/null @@ -1,176 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style srp command -

    -

    Syntax: -

    -

    pair_style srp cutoff btype dist keyword value ... -

    -
    • cutoff = global cutoff for SRP interactions (distance units) - -
    • btype = bond type to apply SRP interactions to (can be wildcard, see below) - -
    • distance = min or mid - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = exclude - -
        exclude value = yes or no 
-
      - -
    -

    Examples: -

    -
    pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
-pair_coeff 1 1 dpd 60.0 4.5 1.0 
-pair_coeff 1 2 none 
-pair_coeff 2 2 srp 100.0 0.8 
-
    -
    pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
-pair_coeff 1 1 dpd 60.0 50 1.0 
-pair_coeff 1 2 none 
-pair_coeff 2 2 srp 40.0 
-
    -
    pair_style hybrid srp 0.8 2 mid 
-pair_coeff 1 1 none 
-pair_coeff 1 2 none 
-pair_coeff 2 2 srp 100.0 0.8 
-
    -

    Description: -

    -

    Style srp computes a soft segmental repulsive potential (SRP) that -acts between pairs of bonds. This potential is useful for preventing -bonds from passing through one another when a soft non-bonded -potential acts between beads in, for example, DPD polymer chains. An -example input script that uses this command is provided in -examples/USER/srp. -

    -

    Bonds of specified type btype interact with one another through a -bond-pairwise potential, such that the force on bond i due to bond -j is as follows -

    -
    -
    -

    where r and rij are the distance and unit vector between the two -bonds. Note that btype can be specified as an asterisk "*", which -case the interaction is applied to all bond types. The mid option -computes r and rij from the midpoint distance between bonds. The -min option computes r and rij from the minimum distance between -bonds. The force acting on a bond is mapped onto the two bond atoms -according to the lever rule, -

    -
    -
    -

    where L is the normalized distance from the atom to the point of -closest approach of bond i and j. The mid option takes L as -0.5 for each interaction as described in (Sirk). -

    -

    The following coefficients must be defined via the -pair_coeff command as in the examples above, or in -the data file or restart file read by the read_data -or read_restart commands: -

    -
    • C (force units) -
    • rc (distance units) -
    -

    The last coefficient is optional. If not specified, the global cutoff -is used. -

    -

    IMPORTANT NOTE: Pair style srp considers each bond of type btype to -be a fictitious "particle" of type bptype, where bptype is the -largest atom type in the system. There cannot be any actual particles -assigned to this atom type. This means you must specify the number of -types in your system to be one larger would normally be the case, -e.g. via the create_box or -read_data commands. These ficitious "bond particles" -are inserted at the beginning of the run, and serve as placeholders -that define the position of the bonds. This allows neighbor lists to -be constructed and pairwise interactions to be computed in almost the -same way as is done for actual particles. Because bonds interact only -with other bonds, pair_style hybrid should be used -to turn off interactions between atom type bptype and all other -types of atoms. An error will be flagged if pair_style -hybrid is not used. -

    -

    The optional exclude keyword determines if forces are computed -between first neighbor (directly connected) bonds. For a setting of -no, first neighbor forces are computed; for yes they are not -computed. A setting of no cannot be used with the min option for -distance calculation because the the minimum distance between directly -connected bonds is zero. -

    -

    Pair style srp turns off normalization of thermodynamic properties -by particle number, as if the command thermo_modify norm -no had been issued. -

    -

    The pairwise energy associated with style srp is shifted to be zero -at the cutoff distance rc. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair styles does not support mixing. -

    -

    This pair style does not support the pair_modify -shift option for the energy of the pair interaction. Note that as -discussed above, the energy term is already shifted to be 0.0 at the -cutoff distance rc. -

    -

    The pair_modify table option is not relevant for -this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes global and per-atom information to binary -restart files. Pair srp should be used with pair_style -hybrid, thus the pair_coeff commands need to be -specified in the input script when reading a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the Making LAMMPS section -for more info. -

    -

    This pair style must be used with pair_style -hybrid. -

    -

    This pair style requires the newton command to be on -for non-bonded interactions. -

    -

    Related commands: -

    -

    pair_style hybrid, pair_coeff, -pair dpd -

    -

    Default: -

    -

    The default keyword value is exclude = yes. -

    -
    - - - -

    (Sirk) Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J -Chem Phys, 136 (13) 134903, 2012. -

    - diff --git a/doc/doc2/pair_style.html b/doc/doc2/pair_style.html deleted file mode 100644 index 95fd464b9a..0000000000 --- a/doc/doc2/pair_style.html +++ /dev/null @@ -1,235 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style command -

    -

    Syntax: -

    -
    pair_style style args 
-
    -
    • style = one of the styles from the list below -
    • args = arguments used by a particular style -
    -

    Examples: -

    -
    pair_style lj/cut 2.5
-pair_style eam/alloy
-pair_style hybrid lj/charmm/coul/long 10.0 eam
-pair_style table linear 1000
-pair_style none 
-
    -

    Description: -

    -

    Set the formula(s) LAMMPS uses to compute pairwise interactions. In -LAMMPS, pair potentials are defined between pairs of atoms that are -within a cutoff distance and the set of active interactions typically -changes over time. See the bond_style command to -define potentials between pairs of bonded atoms, which typically -remain in place for the duration of a simulation. -

    -

    In LAMMPS, pairwise force fields encompass a variety of interactions, -some of which include many-body effects, e.g. EAM, Stillinger-Weber, -Tersoff, REBO potentials. They are still classified as "pairwise" -potentials because the set of interacting atoms changes with time -(unlike molecular bonds) and thus a neighbor list is used to find -nearby interacting atoms. -

    -

    Hybrid models where specified pairs of atom types interact via -different pair potentials can be setup using the hybrid pair style. -

    -

    The coefficients associated with a pair style are typically set for -each pair of atom types, and are specified by the -pair_coeff command or read from a file by the -read_data or read_restart -commands. -

    -

    The pair_modify command sets options for mixing of -type I-J interaction coefficients and adding energy offsets or tail -corrections to Lennard-Jones potentials. Details on these options as -they pertain to individual potentials are described on the doc page -for the potential. Likewise, info on whether the potential -information is stored in a restart file is listed -on the potential doc page. -

    -

    In the formulas listed for each pair style, E is the energy of a -pairwise interaction between two atoms separated by a distance r. -The force between the atoms is the negative derivative of this -expression. -

    -

    If the pair_style command has a cutoff argument, it sets global -cutoffs for all pairs of atom types. The distance(s) can be smaller -or larger than the dimensions of the simulation box. -

    -

    Typically, the global cutoff value can be overridden for a specific -pair of atom types by the pair_coeff command. The -pair style settings (including global cutoffs) can be changed by a -subsequent pair_style command using the same style. This will reset -the cutoffs for all atom type pairs, including those previously set -explicitly by a pair_coeff command. The exceptions -to this are that pair_style table and hybrid settings cannot be -reset. A new pair_style command for these styles will wipe out all -previously specified pair_coeff values. -

    -
    - -

    Here is an alphabetic list of pair styles defined in LAMMPS. They are -also given in more compact form in the pair section of this -page. -

    -

    Click on the style to display the formula it computes, arguments -specified in the pair_style command, and coefficients specified by the -associated pair_coeff command. -

    -

    There are also additional pair styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the pair -section of this page. -

    -

    There are also additional accelerated pair styles (not listed here) -included in the LAMMPS distribution for faster performance on CPUs and -GPUs. The list of these with links to the individual styles are given -in the pair section of this page. -

    - - -
    - -

    Restrictions: -

    -

    This command must be used before any coefficients are set by the -pair_coeff, read_data, or -read_restart commands. -

    -

    Some pair styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info on packages. -The doc pages for individual pair potentials tell if it is part of a -package. -

    -

    Related commands: -

    -

    pair_coeff, read_data, -pair_modify, kspace_style, -dielectric, pair_write -

    -

    Default: -

    -
    pair_style none 
-
    - diff --git a/doc/doc2/pair_sw.html b/doc/doc2/pair_sw.html deleted file mode 100644 index 8a9164f90b..0000000000 --- a/doc/doc2/pair_sw.html +++ /dev/null @@ -1,228 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style sw command -

    -

    pair_style sw/cuda command -

    -

    pair_style sw/gpu command -

    -

    pair_style sw/intel command -

    -

    pair_style sw/kk command -

    -

    pair_style sw/omp command -

    -

    Syntax: -

    -
    pair_style sw 
-
    -

    Examples: -

    -
    pair_style sw
-pair_coeff * * si.sw Si
-pair_coeff * * GaN.sw Ga N Ga 
-
    -

    Description: -

    -

    The sw style computes a 3-body Stillinger-Weber -potential for the energy E of a system of atoms as -

    -
    -
    -

    where phi2 is a two-body term and phi3 is a three-body term. The -summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = a*sigma. -

    -

    Only a single pair_coeff command is used with the sw style which -specifies a Stillinger-Weber potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of SW elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine a file SiC.sw has Stillinger-Weber values for -Si and C. If your LAMMPS simulation has 4 atoms types and you want -the 1st 3 to be Si, and the 4th to be C, you would use the following -pair_coeff command: -

    -
    pair_coeff * * SiC.sw Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the SW file. The final C argument maps LAMMPS atom type 4 -to the C element in the SW file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a sw -potential is used as part of the hybrid pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. -

    -

    Stillinger-Weber files in the potentials directory of the LAMMPS -distribution have a ".sw" suffix. Lines that are not blank or -comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formula above: -

    -
    • element 1 (the center atom in a 3-body interaction) -
    • element 2 -
    • element 3 -
    • epsilon (energy units) -
    • sigma (distance units) -
    • a -
    • lambda -
    • gamma -
    • costheta0 -
    • A -
    • B -
    • p -
    • q -
    • tol -
    -

    The A, B, p, and q parameters are used only for two-body -interactions. The lambda and costheta0 parameters are used only for -three-body interactions. The epsilon, sigma and a parameters are used -for both two-body and three-body interactions. gamma is used only in the -three-body interactions, but is defined for pairs of atoms. -The non-annotated parameters are unitless. -

    -

    LAMMPS introduces an additional performance-optimization parameter tol -that is used for both two-body and three-body interactions. In the -Stillinger-Weber potential, the interaction energies become negligibly -small at atomic separations substantially less than the theoretical -cutoff distances. LAMMPS therefore defines a virtual cutoff distance -based on a user defined tolerance tol. The use of the virtual cutoff -distance in constructing atom neighbor lists can significantly reduce -the neighbor list sizes and therefore the computational cost. LAMMPS -provides a tol value for each of the three-body entries so that they -can be separately controlled. If tol = 0.0, then the standard -Stillinger-Weber cutoff is used. -

    -

    The Stillinger-Weber potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. -

    -

    For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify SW parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. -

    -

    As annotated above, the first element in the entry is the center atom -in a three-body interaction. Thus an entry for SiCC means a Si atom -with 2 C atoms as neighbors. The parameter values used for the -two-body interaction come from the entry where the 2nd and 3rd -elements are the same. Thus the two-body parameters for Si -interacting with C, comes from the SiCC entry. The three-body -parameters can in principle be specific to the three elements of the -configuration. In the literature, however, the three-body parameters -are usually defined by simple formulas involving two sets of pair-wise -parameters, corresponding to the ij and ik pairs, where i is the -center atom. The user must ensure that the correct combining rule is -used to calculate the values of the threebody parameters for -alloys. Note also that the function phi3 contains two exponential -screening factors with parameter values from the ij pair and ik -pairs. So phi3 for a C atom bonded to a Si atom and a second C atom -will depend on the three-body parameters for the CSiC entry, and also -on the two-body parameters for the CCC and CSiSi entries. Since the -order of the two neighbors is arbitrary, the threebody parameters for -entries CSiC and CCSi should be the same. Similarly, the two-body -parameters for entries SiCC and CSiSi should also be the same. The -parameters used only for two-body interactions (A, B, p, and q) in -entries whose 2nd and 3rd element are different (e.g. SiCSi) are not -used for anything and can be set to 0.0 if desired. -This is also true for the parameters in phi3 that are -taken from the ij and ik pairs (sigma, a, gamma) -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    When using the USER-INTEL package with this style, there is an -additional 5 to 10 percent performance improvement when the -Stillinger-Weber parameters p and q are set to 4 and 0 respectively. -These parameters are common for modeling silicon and water. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    The Stillinger-Weber potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal units. -You can use the SW potential with any LAMMPS units, but you would need -to create your own SW potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Stillinger) Stillinger and Weber, Phys Rev B, 31, 5262 (1985). -

    - diff --git a/doc/doc2/pair_table.html b/doc/doc2/pair_table.html deleted file mode 100644 index ea976ba199..0000000000 --- a/doc/doc2/pair_table.html +++ /dev/null @@ -1,263 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style table command -

    -

    pair_style table/gpu command -

    -

    pair_style table/kk command -

    -

    pair_style table/omp command -

    -

    Syntax: -

    -
    pair_style table style N keyword ... 
-
    -
    • style = lookup or linear or spline or bitmap = method of interpolation -
    • N = use N values in lookup, linear, spline tables -
    • N = use 2^N values in bitmap tables -
    • zero or more keywords may be appended -
    • keyword = ewald or pppm or msm or dispersion or tip4p -
    -

    Examples: -

    -
    pair_style table linear 1000
-pair_style table linear 1000 pppm
-pair_style table bitmap 12
-pair_coeff * 3 morse.table ENTRY1
-pair_coeff * 3 morse.table ENTRY1 7.0 
-
    -

    Description: -

    -

    Style table creates interpolation tables of length N from pair -potential and force values listed in a file(s) as a function of -distance. The files are read by the pair_coeff -command. -

    -

    The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and force values at each of N -distances. During a simulation, these tables are used to interpolate -energy and force values as needed. The interpolation is done in one -of 4 styles: lookup, linear, spline, or bitmap. -

    -

    For the lookup style, the distance between 2 atoms is used to find -the nearest table entry, which is the energy or force. -

    -

    For the linear style, the pair distance is used to find 2 -surrounding table values from which an energy or force is computed by -linear interpolation. -

    -

    For the spline style, a cubic spline coefficients are computed and -stored at each of the N values in the table. The pair distance is -used to find the appropriate set of coefficients which are used to -evaluate a cubic polynomial which computes the energy or force. -

    -

    For the bitmap style, the N means to create interpolation tables -that are 2^N in length. The pair distance is used to index into the -table via a fast bit-mapping technique due to (Wolff), and a -linear interpolation is performed between adjacent table values. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above. -

    -
    • filename -
    • keyword -
    • cutoff (distance units) -
    -

    The filename specifies a file containing tabulated energy and force -values. The keyword specifies a section of the file. The cutoff is -an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below. -

    -

    If your tabulated potential(s) are designed to be used as the -short-range part of one of the long-range solvers specified by the -kspace_style command, then you must use one or -more of the optional keywords listed above for the pair_style command. -These are ewald or pppm or msm or dispersion or tip4p. This -is so LAMMPS can insure the short-range potential and long-range -solver are compatible with each other, as it does for other -short-range pair styles, such as pair_style -lj/cut/coul/long. Note that it is up to you to insure -the tabulated values for each pair of atom types has the correct -functional form to be compatible with the matching long-range solver. -

    -
    - -

    Here are some guidelines for using the pair_style table command to -best effect: -

    -
    • Vary the number of table points; you may need to use more than you think -to get good resolution. - -
    • Always use the pair_write command to produce a plot -of what the final interpolated potential looks like. This can show up -interpolation "features" you may not like. - -
    • Start with the linear style; it's the style least likely to have problems. - -
    • Use N in the pair_style command equal to the "N" in the tabulation -file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation -is not needed. See discussion below. - -
    • Make sure that your tabulated forces and tabulated energies are consistent -(dE/dr = -F) along the entire range of r values. - -
    • Use as large an inner cutoff as possible. This avoids fitting splines -to very steep parts of the potential. -
    -
    - -

    The format of a tabulated file is a series of one or more sections, -defined as follows (without the parenthesized comments): -

    -
    # Morse potential for Fe   (one or more comment or blank lines) 
-
    -
    MORSE_FE                   (keyword is first text on line)
-N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
-                           (blank)
-1 1.0 25.5 102.34          (index, r, energy, force)
-2 1.02 23.4 98.5
-...
-500 10.0 0.001 0.003 
-
    -

    A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair_coeff -command. The next line lists (in any order) one or more parameters -for the table. Each parameter is a keyword followed by one or more -numeric values. -

    -

    The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the pair_style table command. Let -Ntable = N in the pair_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and force -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual pair distances. This means that if you want the -interpolation tables of length Ntable to match exactly what is in the -tabulated file (with effectively no preliminary interpolation), you -should set Ntable = Nfile, and use the "RSQ" or "BITMAP" parameter. -The internal table abscissa is RSQ (separation distance squared). -

    -

    All other parameters are optional. If "R" or "RSQ" or "BITMAP" does -not appear, then the distances in each line of the table are used -as-is to perform spline interpolation. In this case, the table values -can be spaced in r uniformly or however you wish to position table -values in regions of large gradients. -

    -

    If used, the parameters "R" or "RSQ" are followed by 2 values rlo -and rhi. If specified, the distance associated with each energy and -force value is computed from these 2 values (at high accuracy), rather -than using the (low-accuracy) value listed in each line of the table. -The distance values in the table file are ignored in this case. -For "R", distances uniformly spaced between rlo and rhi are -computed; for "RSQ", squared distances uniformly spaced between -rlo*rlo and rhi*rhi are computed. -

    -

    If used, the parameter "BITMAP" is also followed by 2 values rlo and -rhi. These values, along with the "N" value determine the ordering -of the N lines that follow and what distance is associated with each. -This ordering is complex, so it is not documented here, since this -file is typically produced by the pair_write command -with its bitmap option. When the table is in BITMAP format, the "N" -parameter in the file must be equal to 2^M where M is the value -specified in the pair_style command. Also, a cutoff parameter cannot -be used as an optional 3rd argument in the pair_coeff command; the -entire table extent as specified in the file must be used. -

    -

    If used, the parameter "FPRIME" is followed by 2 values fplo and -fphi which are the derivative of the force at the innermost and -outermost distances listed in the table. These values are needed by -the spline construction routines. If not specified by the "FPRIME" -parameter, they are estimated (less accurately) by the first 2 and -last 2 force values in the table. This parameter is not used by -BITMAP tables. -

    -

    Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in distance units), the 3rd value is the energy (in energy units), -and the 4th is the force (in force units). The r values must increase -from one line to the next (unless the BITMAP parameter is specified). -

    -

    Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -

    -

    The pair_modify shift, table, and tail options are -not relevant for this pair style. -

    -

    This pair style writes the settings for the "pair_style table" command -to binary restart files, so a pair_style command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair_coeff -commands do need to be specified in the restart input script. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Wolff) Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). -

    - diff --git a/doc/doc2/pair_tersoff.html b/doc/doc2/pair_tersoff.html deleted file mode 100644 index 4e4540c87e..0000000000 --- a/doc/doc2/pair_tersoff.html +++ /dev/null @@ -1,267 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style tersoff command -

    -

    pair_style tersoff/table command -

    -

    pair_style tersoff/cuda -

    -

    pair_style tersoff/gpu -

    -

    pair_style tersoff/kk -

    -

    pair_style tersoff/omp -

    -

    pair_style tersoff/table/omp command -

    -

    Syntax: -

    -
    pair_style style 
-
    -

    style = tersoff or tersoff/table or tersoff/cuda or tersoff/gpu or tersoff/omp or tersoff/table/omp -

    -

    Examples: -

    -
    pair_style tersoff
-pair_coeff * * Si.tersoff Si
-pair_coeff * * SiC.tersoff Si C Si 
-
    -
    pair_style tersoff/table
-pair_coeff * * SiCGe.tersoff Si(D) 
-
    -

    Description: -

    -

    The tersoff style computes a 3-body Tersoff potential -(Tersoff_1) for the energy E of a system of atoms as -

    -
    -
    -

    where f_R is a two-body term and f_A includes three-body interactions. -The summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = R + D. -

    -

    The tersoff/table style uses tabulated forms for the two-body, -environment and angular functions. Linear interpolation is performed -between adjacent table entries. The table length is chosen to be -accurate within 10^-6 with respect to the tersoff style energy. -The tersoff/table should give better performance in terms of speed. -

    -

    Only a single pair_coeff command is used with the tersoff style -which specifies a Tersoff potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of Tersoff elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine the SiC.tersoff file has Tersoff values for Si -and C. If your LAMMPS simulation has 4 atoms types and you want the -1st 3 to be Si, and the 4th to be C, you would use the following -pair_coeff command: -

    -
    pair_coeff * * SiC.tersoff Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the Tersoff file. The final C argument maps LAMMPS atom -type 4 to the C element in the Tersoff file. If a mapping value is -specified as NULL, the mapping is not performed. This can be used -when a tersoff potential is used as part of the hybrid pair style. -The NULL values are placeholders for atom types that will be used with -other potentials. -

    -

    Tersoff files in the potentials directory of the LAMMPS distribution -have a ".tersoff" suffix. Lines that are not blank or comments -(starting with #) define parameters for a triplet of elements. The -parameters in a single entry correspond to coefficients in the formula -above: -

    -
    • element 1 (the center atom in a 3-body interaction) -
    • element 2 (the atom bonded to the center atom) -
    • element 3 (the atom influencing the 1-2 bond in a bond-order sense) -
    • m -
    • gamma -
    • lambda3 (1/distance units) -
    • c -
    • d -
    • costheta0 (can be a value < -1 or > 1) -
    • n -
    • beta -
    • lambda2 (1/distance units) -
    • B (energy units) -
    • R (distance units) -
    • D (distance units) -
    • lambda1 (1/distance units) -
    • A (energy units) -
    -

    The n, beta, lambda2, B, lambda1, and A parameters are only used for -two-body interactions. The m, gamma, lambda3, c, d, and costheta0 -parameters are only used for three-body interactions. The R and D -parameters are used for both two-body and three-body interactions. The -non-annotated parameters are unitless. The value of m must be 3 or 1. -

    -

    The Tersoff potential file must contain entries for all the elements -listed in the pair_coeff command. It can also contain entries for -additional elements not being used in a particular simulation; LAMMPS -ignores those entries. -

    -

    For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify Tersoff parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. -

    -

    As annotated above, the first element in the entry is the center atom -in a three-body interaction and it is bonded to the 2nd atom and the -bond is influenced by the 3rd atom. Thus an entry for SiCC means Si -bonded to a C with another C atom influencing the bond. Thus -three-body parameters for SiCSi and SiSiC entries will not, in -general, be the same. The parameters used for the two-body -interaction come from the entry where the 2nd element is repeated. -Thus the two-body parameters for Si interacting with C, comes from the -SiCC entry. -

    -

    The parameters used for a particular -three-body interaction come from the entry with the corresponding -three elements. The parameters used only for two-body interactions -(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd -element are different (e.g. SiCSi) are not used for anything and can -be set to 0.0 if desired. -

    -

    Note that the twobody parameters in entries such as SiCC and CSiSi -are often the same, due to the common use of symmetric mixing rules, -but this is not always the case. For example, the beta and n parameters in -Tersoff_2 (Tersoff_2) are not symmetric. -

    -

    We chose the above form so as to enable users to define all commonly -used variants of the Tersoff potential. In particular, our form -reduces to the original Tersoff form when m = 3 and gamma = 1, while -it reduces to the form of Albe et al. when beta = 1 and m = 1. -Note that in the current Tersoff implementation in LAMMPS, m must be -specified as either 3 or 1. Tersoff used a slightly different but -equivalent form for alloys, which we will refer to as Tersoff_2 -potential (Tersoff_2). The tersoff/table style implements -Tersoff_2 parameterization only. -

    -

    LAMMPS parameter values for Tersoff_2 can be obtained as follows: -gamma_ijk = omega_ik, lambda3 = 0 and the value of -m has no effect. The parameters for species i and j can be calculated -using the Tersoff_2 mixing rules: -

    -
    -
    -

    Tersoff_2 parameters R and S must be converted to the LAMMPS -parameters R and D (R is different in both forms), using the following -relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the -Tersoff_2 parameters. -

    -

    In the potentials directory, the file SiCGe.tersoff provides the -LAMMPS parameters for Tersoff's various versions of Si, as well as his -alloy parameters for Si, C, and Ge. This file can be used for pure Si, -(three different versions), pure C, pure Ge, binary SiC, and binary -SiGe. LAMMPS will generate an error if this file is used with any -combination involving C and Ge, since there are no entries for the GeC -interactions (Tersoff did not publish parameters for this -cross-interaction.) Tersoff files are also provided for the SiC alloy -(SiC.tersoff) and the GaN (GaN.tersoff) alloys. -

    -

    Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou -for helping clarify how Tersoff parameters for alloys have been -defined in various papers. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    The Tersoff potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal units. You can -use the Tersoff potential with any LAMMPS units, but you would need to -create your own Tersoff potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Tersoff_1) J. Tersoff, Phys Rev B, 37, 6991 (1988). -

    - - -

    (Albe) J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: -Condens. Matter, 15, 5649(2003). -

    - - -

    (Tersoff_2) J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) -

    - diff --git a/doc/doc2/pair_tersoff_mod.html b/doc/doc2/pair_tersoff_mod.html deleted file mode 100644 index 2e6a5a366b..0000000000 --- a/doc/doc2/pair_tersoff_mod.html +++ /dev/null @@ -1,204 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style tersoff/mod command -

    -

    pair_style tersoff/mod/kk command -

    -

    pair_style tersoff/mod/omp command -

    -

    Syntax: -

    -
    pair_style tersoff/mod 
-
    -

    Examples: -

    -
    pair_style tersoff/mod
-pair_coeff * * Si.tersoff.mod Si Si 
-
    -

    Description: -

    -

    The tersoff/mod style computes a bond-order type interatomic -potential (Kumagai) based on a 3-body Tersoff potential -(Tersoff_1), (Tersoff_2) with modified -cutoff function and angular-dependent term, giving the energy E of a -system of atoms as -

    -
    -
    -

    where f_R is a two-body term and f_A includes three-body interactions. -The summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = R + D. -

    -

    The modified cutoff function f_C proposed by (Murty) and -having a continuous second-order differential is employed. The -angular-dependent term g(theta) was modified to increase the -flexibility of the potential. -

    -

    The tersoff/mod potential is fitted to both the elastic constants -and melting point by employing the modified Tersoff potential function -form in which the angular-dependent term is improved. The model -performs extremely well in describing the crystalline, liquid, and -amorphous phases (Schelling). -

    -

    Only a single pair_coeff command is used with the tersoff/mod style -which specifies a Tersoff/MOD potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of Tersoff/MOD elements to atom types -
    -

    As an example, imagine the Si.tersoff_mod file has Tersoff values for Si. -If your LAMMPS simulation has 3 Si atoms types, you would use the following -pair_coeff command: -

    -
    pair_coeff * * Si.tersoff_mod Si Si Si 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The three Si arguments map LAMMPS atom types 1,2,3 to the Si element -in the Tersoff/MOD file. If a mapping value is specified as NULL, the -mapping is not performed. This can be used when a tersoff/mod -potential is used as part of the hybrid pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. -

    -

    Tersoff/MOD file in the potentials directory of the LAMMPS -distribution have a ".tersoff.mod" suffix. Lines that are not blank -or comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to coefficients -in the formula above: -

    -
    • element 1 (the center atom in a 3-body interaction) -
    • element 2 (the atom bonded to the center atom) -
    • element 3 (the atom influencing the 1-2 bond in a bond-order sense) -
    • beta -
    • alpha -
    • h -
    • eta -
    • beta_ters = 1 (dummy parameter) -
    • lambda2 (1/distance units) -
    • B (energy units) -
    • R (distance units) -
    • D (distance units) -
    • lambda1 (1/distance units) -
    • A (energy units) -
    • n -
    • c1 -
    • c2 -
    • c3 -
    • c4 -
    • c5 -
    -

    The n, eta, lambda2, B, lambda1, and A parameters are only used for -two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h -parameters are only used for three-body interactions. The R and D -parameters are used for both two-body and three-body interactions. The -non-annotated parameters are unitless. -

    -

    The Tersoff/MOD potential file must contain entries for all the elements -listed in the pair_coeff command. It can also contain entries for -additional elements not being used in a particular simulation; LAMMPS -ignores those entries. -

    -

    For a single-element simulation, only a single entry is required -(e.g. SiSiSi). As annotated above, the first element in the entry is -the center atom in a three-body interaction and it is bonded to the -2nd atom and the bond is influenced by the 3rd atom. Thus an entry -for SiSiSi means Si bonded to a Si with another Si atom influencing the bond. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    The Tersoff/MOD potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal units. You can -use the Tersoff/MOD potential with any LAMMPS units, but you would need to -create your own Tersoff/MOD potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Kumagai) T. Kumagai, S. Izumi, S. Hara, S. Sakai, -Comp. Mat. Science, 39, 457 (2007). -

    - - -

    (Tersoff_1) J. Tersoff, Phys Rev B, 37, 6991 (1988). -

    - - -

    (Tersoff_2) J. Tersoff, Phys Rev B, 38, 9902 (1988). -

    - - -

    (Murty) M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995). -

    - - -

    (Schelling) Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008). -

    - diff --git a/doc/doc2/pair_tersoff_zbl.html b/doc/doc2/pair_tersoff_zbl.html deleted file mode 100644 index 3374f89148..0000000000 --- a/doc/doc2/pair_tersoff_zbl.html +++ /dev/null @@ -1,278 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style tersoff/zbl command -

    -

    pair_style tersoff/zbl/kk command -

    -

    pair_style tersoff/zbl/omp command -

    -

    Syntax: -

    -
    pair_style tersoff/zbl 
-
    -

    Examples: -

    -
    pair_style tersoff/zbl
-pair_coeff * * SiC.tersoff.zbl Si C Si 
-
    -

    Description: -

    -

    The tersoff/zbl style computes a 3-body Tersoff potential -(Tersoff_1) with a close-separation pairwise modification -based on a Coulomb potential and the Ziegler-Biersack-Littmark -universal screening function (ZBL), giving the energy E of a -system of atoms as -

    -
    -
    -

    The f_F term is a fermi-like function used to smoothly connect the ZBL -repulsive potential with the Tersoff potential. There are 2 -parameters used to adjust it: A_F and r_C. A_F controls how "sharp" -the transition is between the two, and r_C is essentially the cutoff -for the ZBL potential. -

    -

    For the ZBL portion, there are two terms. The first is the Coulomb -repulsive term, with Z1, Z2 as the number of protons in each nucleus, -e as the electron charge (1 for metal and real units) and epsilon0 as -the permittivity of vacuum. The second part is the ZBL universal -screening function, with a0 being the Bohr radius (typically 0.529 -Angstroms), and the remainder of the coefficients provided by the -original paper. This screening function should be applicable to most -systems. However, it is only accurate for small separations -(i.e. less than 1 Angstrom). -

    -

    For the Tersoff portion, f_R is a two-body term and f_A includes -three-body interactions. The summations in the formula are over all -neighbors J and K of atom I within a cutoff distance = R + D. -

    -

    Only a single pair_coeff command is used with the tersoff/zbl style -which specifies a Tersoff/ZBL potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of Tersoff/ZBL elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values -for Si and C. If your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be Si, and the 4th to be C, you would use the -following pair_coeff command: -

    -
    pair_coeff * * SiC.tersoff Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the Tersoff/ZBL file. The final C argument maps LAMMPS -atom type 4 to the C element in the Tersoff/ZBL file. If a mapping -value is specified as NULL, the mapping is not performed. This can be -used when a tersoff/zbl potential is used as part of the hybrid -pair style. The NULL values are placeholders for atom types that will -be used with other potentials. -

    -

    Tersoff/ZBL files in the potentials directory of the LAMMPS -distribution have a ".tersoff.zbl" suffix. Lines that are not blank -or comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to coefficients -in the formula above: -

    -
    • element 1 (the center atom in a 3-body interaction) -
    • element 2 (the atom bonded to the center atom) -
    • element 3 (the atom influencing the 1-2 bond in a bond-order sense) -
    • m -
    • gamma -
    • lambda3 (1/distance units) -
    • c -
    • d -
    • costheta0 (can be a value < -1 or > 1) -
    • n -
    • beta -
    • lambda2 (1/distance units) -
    • B (energy units) -
    • R (distance units) -
    • D (distance units) -
    • lambda1 (1/distance units) -
    • A (energy units) -
    • Z_i -
    • Z_j -
    • ZBLcut (distance units) -
    • ZBLexpscale (1/distance units) -
    -

    The n, beta, lambda2, B, lambda1, and A parameters are only used for -two-body interactions. The m, gamma, lambda3, c, d, and costheta0 -parameters are only used for three-body interactions. The R and D -parameters are used for both two-body and three-body interactions. The -Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive -portion of the potential and in the Fermi-like function. The -non-annotated parameters are unitless. The value of m must be 3 or 1. -

    -

    The Tersoff/ZBL potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. -

    -

    For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify Tersoff parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. -

    -

    As annotated above, the first element in the entry is the center atom -in a three-body interaction and it is bonded to the 2nd atom and the -bond is influenced by the 3rd atom. Thus an entry for SiCC means Si -bonded to a C with another C atom influencing the bond. Thus -three-body parameters for SiCSi and SiSiC entries will not, in -general, be the same. The parameters used for the two-body -interaction come from the entry where the 2nd element is repeated. -Thus the two-body parameters for Si interacting with C, comes from the -SiCC entry. -

    -

    The parameters used for a particular -three-body interaction come from the entry with the corresponding -three elements. The parameters used only for two-body interactions -(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd -element are different (e.g. SiCSi) are not used for anything and can -be set to 0.0 if desired. -

    -

    Note that the twobody parameters in entries such as SiCC and CSiSi -are often the same, due to the common use of symmetric mixing rules, -but this is not always the case. For example, the beta and n parameters in -Tersoff_2 (Tersoff_2) are not symmetric. -

    -

    We chose the above form so as to enable users to define all commonly -used variants of the Tersoff portion of the potential. In particular, -our form reduces to the original Tersoff form when m = 3 and gamma = -1, while it reduces to the form of Albe et al. when beta = 1 -and m = 1. Note that in the current Tersoff implementation in LAMMPS, -m must be specified as either 3 or 1. Tersoff used a slightly -different but equivalent form for alloys, which we will refer to as -Tersoff_2 potential (Tersoff_2). -

    -

    LAMMPS parameter values for Tersoff_2 can be obtained as follows: -gamma = omega_ijk, lambda3 = 0 and the value of -m has no effect. The parameters for species i and j can be calculated -using the Tersoff_2 mixing rules: -

    -
    -
    -

    Tersoff_2 parameters R and S must be converted to the LAMMPS -parameters R and D (R is different in both forms), using the following -relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the -Tersoff_2 parameters. -

    -

    In the potentials directory, the file SiCGe.tersoff provides the -LAMMPS parameters for Tersoff's various versions of Si, as well as his -alloy parameters for Si, C, and Ge. This file can be used for pure Si, -(three different versions), pure C, pure Ge, binary SiC, and binary -SiGe. LAMMPS will generate an error if this file is used with any -combination involving C and Ge, since there are no entries for the GeC -interactions (Tersoff did not publish parameters for this -cross-interaction.) Tersoff files are also provided for the SiC alloy -(SiC.tersoff) and the GaN (GaN.tersoff) alloys. -

    -

    Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou -for helping clarify how Tersoff parameters for alloys have been -defined in various papers. Also thanks to Ram Devanathan for -providing the base ZBL implementation. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    The Tersoff/ZBL potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal units. -You can use the Tersoff potential with any LAMMPS units, but you would -need to create your own Tersoff potential file with coefficients -listed in the appropriate units if your simulation doesn't use "metal" -units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Tersoff_1) J. Tersoff, Phys Rev B, 37, 6991 (1988). -

    - - -

    (ZBL) J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges -of Ions in Matter' Vol 1, 1985, Pergamon Press. -

    - - -

    (Albe) J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.: -Condens. Matter, 15, 5649(2003). -

    - - -

    (Tersoff_2) J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) -

    - diff --git a/doc/doc2/pair_thole.html b/doc/doc2/pair_thole.html deleted file mode 100644 index 2fa01d9e86..0000000000 --- a/doc/doc2/pair_thole.html +++ /dev/null @@ -1,133 +0,0 @@ - - - - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style thole command -

    -

    Syntax: -

    -
    pair_style thole damp cutoff 
-
    -
    • thole = style name -
    • damp = global damping parameter -
    • cutoff = global cutoff -
    -

    Examples: -

    -
    pair_style hybrid/overlay ... thole 2.6 12.0
-pair_coeff 1 1 thole 1.0
-pair_coeff 1 2 thole 1.0 2.6 10.0
-pair_coeff * 2 thole 1.0 2.6 
-
    -

    Description: -

    -

    The thole pair style is meant to be used with force fields that -include explicit polarization through Drude dipoles. This link -describes how to use the thermalized Drude oscillator -model in LAMMPS and polarizable models in LAMMPS -are discussed in this Section. -

    -

    The thole pair style should be used as a sub-style within in the -pair_hybrid/overlay command, in conjunction with a -main pair style including Coulomb interactions, i.e. any pair style -containing coul/cut or coul/long in its style name. -

    -

    The thole pair style computes the Coulomb interaction damped at -short distances by a function -

    -

    \begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 + -\frac{s_{ij} r_{ij} }{2} \right) -\exp \left( - s_{ij} r_{ij} \right) \end{equation} -

    -

    This function results from an adaptation to point charges -(Noskov) of the dipole screening scheme originally proposed -by Thole. The scaling coefficient \(s_{ij} \) is determined -by the polarizability of the atoms, \( \alpha_i \), and by a Thole -damping parameter \( a \). This Thole damping parameter usually takes -a value of 2.6, but in certain force fields the value can depend upon -the atom types. The mixing rule for Thole damping parameters is the -arithmetic average, and for polarizabilities the geometric average -between the atom-specific values. -

    -

    \begin{equation} s_{ij} = \frac{ a_{ij} }{ -(\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{ -[(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation} -

    -

    The damping function is only applied to the interactions between the -point charges representing the induced dipoles on polarizable sites, -that is, charges on Drude particles, \( q_{D,i} \), and opposite -charges, \( -q_{D,i} \), located on the respective core particles -(to which each Drude particle is bonded). Therefore, Thole screening -is not applied to the full charge of the core particle \( q_i \), but -only to the \( -q_{D,i} \) part of it. -

    -

    The interactions between core charges are subject to the weighting -factors set by the special_bonds command. The -interactions between Drude particles and core charges or -non-polarizable atoms are also subject to these weighting factors. The -Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from -their respective cores. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the example -above. -

    -
    • alpha (distance units^3) -
    • damp -
    • cutoff (distance units) -
    -

    The last two coefficients are optional. If not specified the global -Thole damping parameter or global cutoff specified in the pair_style -command are used. In order to specify a cutoff (third argument) a damp -parameter (second argument) must also be specified. -

    -

    Mixing: -

    -

    The thole pair style does not support mixing. Thus, coefficients -for all I,J pairs must be specified explicitly. -

    -

    Restrictions: -

    -

    These pair styles are part of the USER-DRUDE package. They are only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This pair_style should currently not be used with the charmm dihedral -style if the latter non-zero 1-4 weighting -factors. This is because the thole pair style does not know which -pairs are 1-4 partners of which dihedrals. -

    -

    Related commands: -

    -

    fix drude, fix -langevin/drude, fix -drude/transform, compute -temp/drude -

    -

    Default: none -

    -
    - - - -

    (Noskov) Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). -

    - - -

    (Thole) Chem Phys, 59, 341 (1981). -

    - diff --git a/doc/doc2/pair_tri_lj.html b/doc/doc2/pair_tri_lj.html deleted file mode 100644 index 98a230c736..0000000000 --- a/doc/doc2/pair_tri_lj.html +++ /dev/null @@ -1,145 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style tri/lj command -

    -

    pair_style tri/lj/omp command -

    -

    Syntax: -

    -
    pair_style tri/lj cutoff 
-
    -

    cutoff = global cutoff for interactions (distance units) -

    -

    Examples: -

    -
    pair_style tri/lj 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5 
-
    -

    Description: -

    -

    Style tri/lj treats particles which are triangles as a set of small -spherical particles that tile the triangle surface as explained below. -Interactions between two triangles, each with N1 and N2 spherical -particles, are calculated as the pairwise sum of N1*N2 Lennard-Jones -interactions. Interactions between a triangle with N spherical -particles and a point particle are treated as the pairwise sum of N -Lennard-Jones interactions. See the pair_style lj/cut -doc page for the definition of Lennard-Jones interactions. -

    -

    The cutoff distance for an interaction between 2 triangles, or between -a triangle and a point particle, is calculated from the position of -the triangle (its centroid), not between pairs of individual spheres -comprising the triangle. Thus an interaction is either calculated in -its entirety or not at all. -

    -

    The set of non-overlapping spherical particles that represent a -triangle, for purposes of this pair style, are generated in the -following manner. Assume the triangle is of type I, and sigma_II has -been specified. We want a set of spheres with centers in the plane of -the triangle, none of them larger in diameter than sigma_II, which -completely cover the triangle's area, but with minimial overlap and a -minimal total number of spheres. This is done in a recursive manner. -Place a sphere at the centroid of the original triangle. Calculate -what diameter it must have to just cover all 3 corner points of the -triangle. If that diameter is equal to or smaller than sigma_II, then -include a sphere of the calculated diameter in the set of covering -spheres. It the diameter is larger than sigma_II, then split the -triangle into 2 triangles by bisecting its longest side. Repeat the -process on each sub-triangle, recursing as far as needed to generate a -set of covering spheres. When finished, the original criteria are -met, and the set of covering spheres shoule be near minimal in number -and overlap, at least for input triangles with a reasonable -aspect-ratio. -

    -

    The LJ interaction between 2 spheres on different triangles of types -I,J is computed with an arithmetic mixing of the sigma values of the 2 -spheres and using the specified epsilon value for I,J atom types. -Note that because the sigma values for triangles spheres is computed -using only sigma_II values, specific to the triangles's type, this -means that any specified sigma_IJ values (for I != J) are effectively -ignored. -

    -

    For style tri/lj, the following coefficients must be defined for -each pair of atoms types via the pair_coeff command -as in the examples above, or in the data file or restart files read by -the read_data or read_restart -commands: -

    -
    • epsilon (energy units) -
    • sigma (distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global cutoff -is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of this pair style can be mixed. The -default mix value is geometric. See the "pair_modify" command for -details. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Defining particles to be triangles so they participate in tri/tri or -tri/particle interactions requires the use the atom_style -tri command. -

    -

    Related commands: -

    -

    pair_coeff, pair_style line/lj -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_vashishta.html b/doc/doc2/pair_vashishta.html deleted file mode 100644 index 7a5832c683..0000000000 --- a/doc/doc2/pair_vashishta.html +++ /dev/null @@ -1,236 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style vashishta command -

    -

    pair_style vashishta/omp command -

    -

    Syntax: -

    -
    pair_style vashishta 
-
    -

    Examples: -

    -
    pair_style vashishta
-pair_coeff * * SiC.vashishta Si C 
-
    -

    Description: -

    -

    The vashishta style computes the combined 2-body and 3-body -family of potentials developed in the group of Vashishta and -co-workers. By combining repulsive, screened Coulombic, -screened charge-dipole, and dispersion interactions with a -bond-angle energy based on the Stillinger-Weber potential, -this potential has been used to describe a variety of inorganic -compounds, including SiO2 Vashishta1990, -SiC Vashishta2007, -and InP Branicio2009. -

    -

    The potential for the energy U of a system of atoms is -

    -
    -
    -

    where we follow the notation used in Branicio2009. -U2 is a two-body term and U3 is a three-body term. The -summation over two-body terms is over all neighbors J within -a cutoff distance = rc. The twobody terms are shifted and -tilted by a linear function so that the energy and force are -both zero at rc. The summation over three-body terms -is over all neighbors J and K within a cut-off distance = r0, -where the exponential screening function becomes zero. -

    -

    Only a single pair_coeff command is used with the vashishta style which -specifies a Vashishta potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

    -
    • filename -
    • N element names = mapping of Vashishta elements to atom types -
    -

    See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

    -

    As an example, imagine a file SiC.vashishta has parameters for -Si and C. If your LAMMPS simulation has 4 atoms types and you want -the 1st 3 to be Si, and the 4th to be C, you would use the following -pair_coeff command: -

    -
    pair_coeff * * SiC.vashishta Si Si Si C 
-
    -

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the file. The final C argument maps LAMMPS atom type 4 -to the C element in the file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a vashishta -potential is used as part of the hybrid pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. -

    -

    Vashishta files in the potentials directory of the LAMMPS -distribution have a ".vashishta" suffix. Lines that are not blank or -comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formulae above: -

    -
    • element 1 (the center atom in a 3-body interaction) -
    • element 2 -
    • element 3 -
    • H (energy units) -
    • eta -
    • Zi (electron charge units) -
    • Zj (electron charge units) -
    • lambda1 (distance units) -
    • D (energy units) -
    • lambda4 (distance units) -
    • W (energy units) -
    • rc (distance units) -
    • B (energy units) -
    • gamma -
    • r0 (distance units) -
    • C -
    • costheta0 -
    -

    The non-annotated parameters are unitless. -The Vashishta potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. -For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. -

    -

    Depending on the particular version of the Vashishta potential, -the values of these parameters may be keyed to the identities of -zero, one, two, or three elements. -In order to make the input file format unambiguous, general, -and simple to code, -LAMMPS uses a slightly confusing method for specifying parameters. -All parameters are divided into two classes: two-body and three-body. -Two-body and three-body parameters are handled differently, -as described below. -The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0. -They appear in the above formulae with two subscripts. -The parameters Zi and Zj are also classified as two-body parameters, -even though they only have 1 subscript. -The three-body parameters are B, C, costheta0. -They appear in the above formulae with three subscripts. -Two-body and three-body parameters are handled differently, -as described below. -

    -

    The first element in each entry is the center atom -in a three-body interaction, while the second and third elements -are two neighbor atoms. Three-body parameters for a central atom I -and two neighbors J and K are taken from the IJK entry. -Note that even though three-body parameters do not depend on the order of -J and K, LAMMPS stores three-body parameters for both IJK and IKJ. -The user must ensure that these values are equal. -Two-body parameters for an atom I interacting with atom J are taken from -the IJJ entry, where the 2nd and 3rd -elements are the same. Thus the two-body parameters -for Si interacting with C come from the SiCC entry. Note that even -though two-body parameters (except possibly gamma and r0 in U3) -do not depend on the order of the two elements, -LAMMPS will get the Si-C value from the SiCC entry -and the C-Si value from the CSiSi entry. The user must ensure -that these values are equal. Two-body parameters appearing -in entries where the 2nd and 3rd elements are different are -stored but never used. It is good practice to enter zero for -these values. Note that the three-body function U3 above -contains the two-body parameters gamma and r0. So U3 for a -central C atom bonded to an Si atom and a second C atom -will take three-body parameters from the CSiC entry, but -two-body parameters from the CCC and CSiSi entries. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. -

    -

    This pair style does not support the pair_modify -shift, table, and tail options. -

    -

    This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

    -

    This pair style requires the newton setting to be "on" -for pair interactions. -

    -

    The Vashishta potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal units. -You can use the Vashishta potential with any LAMMPS units, but you would need -to create your own Vashishta potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Vashishta1990) P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990). -

    - - -

    (Vashishta2007) P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007). -

    - - -

    (Branicio2009) Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002 -

    - diff --git a/doc/doc2/pair_write.html b/doc/doc2/pair_write.html deleted file mode 100644 index f392444416..0000000000 --- a/doc/doc2/pair_write.html +++ /dev/null @@ -1,83 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_write command -

    -

    Syntax: -

    -
    pair_write itype jtype N style inner outer file keyword Qi Qj 
-
    -
    • itype,jtype = 2 atom types -
    • N = # of values -
    • style = r or rsq or bitmap -
    • inner,outer = inner and outer cutoff (distance units) -
    • file = name of file to write values to -
    • keyword = section name in file for this set of tabulated values -
    • Qi,Qj = 2 atom charges (charge units) (optional) -
    -

    Examples: -

    -
    pair_write 1 3 500 r 1.0 10.0 table.txt LJ
-pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5 
-
    -

    Description: -

    -

    Write energy and force values to a file as a function of distance for -the currently defined pair potential. This is useful for plotting the -potential function or otherwise debugging its values. If the file -already exists, the table of values is appended to the end of the file -to allow multiple tables of energy and force to be included in one -file. -

    -

    The energy and force values are computed at distances from inner to -outer for 2 interacting atoms of type itype and jtype, using the -appropriate pair_coeff coefficients. If the style -is r, then N distances are used, evenly spaced in r; if the style is -rsq, N distances are used, evenly spaced in r^2. -

    -

    For example, for N = 7, style = r, inner = 1.0, and outer = 4.0, -values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. -

    -

    If the style is bitmap, then 2^N values are written to the file in a -format and order consistent with how they are read in by the -pair_coeff command for pair style table. For -reasonable accuracy in a bitmapped table, choose N >= 12, an inner -value that is smaller than the distance of closest approach of 2 -atoms, and an outer value <= cutoff of the potential. -

    -

    If the pair potential is computed between charged atoms, the charges -of the pair of interacting atoms can optionally be specified. If not -specified, values of Qi = Qj = 1.0 are used. -

    -

    The file is written in the format used as input for the -pair_style table option with keyword as the -section name. Each line written to the file lists an index number -(1-N), a distance (in distance units), an energy (in energy units), -and a force (in force units). -

    -

    Restrictions: -

    -

    All force field coefficients for pair and other kinds of interactions -must be set before this command can be invoked. -

    -

    Due to how the pairwise force is computed, an inner value > 0.0 must -be specified even if the potential has a finite value at r = 0.0. -

    -

    For EAM potentials, the pair_write command only tabulates the -pairwise portion of the potential, not the embedding portion. -

    -

    Related commands: -

    -

    pair_style, pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_yukawa.html b/doc/doc2/pair_yukawa.html deleted file mode 100644 index d4c78f82de..0000000000 --- a/doc/doc2/pair_yukawa.html +++ /dev/null @@ -1,111 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style yukawa command -

    -

    pair_style yukawa/gpu command -

    -

    pair_style yukawa/omp command -

    -

    Syntax: -

    -
    pair_style yukawa kappa cutoff 
-
    -
    • kappa = screening length (inverse distance units) -
    • cutoff = global cutoff for Yukawa interactions (distance units) -
    -

    Examples: -

    -
    pair_style yukawa 2.0 2.5
-pair_coeff 1 1 100.0 2.3
-pair_coeff * * 100.0 
-
    -

    Description: -

    -

    Style yukawa computes pairwise interactions with the formula -

    -
    -
    -

    Rc is the cutoff. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • A (energy*distance units) -
    • cutoff (distance units) -
    -

    The last coefficient is optional. If not specified, the global yukawa -cutoff is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the A coefficient and cutoff -distance for this pair style can be mixed. A is an energy value mixed -like a LJ epsilon. The default mix value is geometric. See the -"pair_modify" command for details. -

    -

    This pair style supports the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    - diff --git a/doc/doc2/pair_yukawa_colloid.html b/doc/doc2/pair_yukawa_colloid.html deleted file mode 100644 index 595e761358..0000000000 --- a/doc/doc2/pair_yukawa_colloid.html +++ /dev/null @@ -1,163 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style yukawa/colloid command -

    -

    pair_style yukawa/colloid/gpu command -

    -

    pair_style yukawa/colloid/omp command -

    -

    Syntax: -

    -
    pair_style yukawa/colloid kappa cutoff 
-
    -
    • kappa = screening length (inverse distance units) -
    • cutoff = global cutoff for colloidal Yukawa interactions (distance units) -
    -

    Examples: -

    -
    pair_style yukawa/colloid 2.0 2.5
-pair_coeff 1 1 100.0 2.3
-pair_coeff * * 100.0 
-
    -

    Description: -

    -

    Style yukawa/colloid computes pairwise interactions with the formula -

    -
    -
    -

    where Ri and Rj are the radii of the two particles and Rc is the -cutoff. -

    -

    In contrast to pair_style yukawa, this functional -form arises from the Coulombic interaction between two colloid -particles, screened due to the presence of an electrolyte, see the -book by Safran for a derivation in the context of DVLO -theory. Pair_style yukawa is a screened Coulombic -potential between two point-charges and uses no such approximation. -

    -

    This potential applies to nearby particle pairs for which the Derjagin -approximation holds, meaning h << Ri + Rj, where h is the -surface-to-surface separation of the two particles. -

    -

    When used in combination with pair_style colloid, -the two terms become the so-called DLVO potential, which combines -electrostatic repulsion and van der Waals attraction. -

    -

    The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -

    -
    • A (energy/distance units) -
    • cutoff (distance units) -
    -

    The prefactor A is determined from the relationship between surface -charge and surface potential due to the presence of electrolyte. Note -that the A for this potential style has different units than the A -used in pair_style yukawa. For low surface -potentials, i.e. less than about 25 mV, A can be written as: -

    -
    A = 2 * PI * R*eps*eps0 * kappa * psi^2 
-
    -

    where -

    -
    • R = colloid radius (distance units) -
    • eps0 = permittivity of free space (charge^2/energy/distance units) -
    • eps = relative permittivity of fluid medium (dimensionless) -
    • kappa = inverse screening length (1/distance units) -
    • psi = surface potential (energy/charge units) -
    -

    The last coefficient is optional. If not specified, the global -yukawa/colloid cutoff is used. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the A coefficient and cutoff -distance for this pair style can be mixed. A is an energy value mixed -like a LJ epsilon. The default mix value is geometric. See the -"pair_modify" command for details. -

    -

    This pair style supports the pair_modify shift -option for the energy of the pair interaction. -

    -

    The pair_modify table option is not relevant -for this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure. -

    -

    This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: -

    -

    This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    This pair style requires that atoms be finite-size spheres with a -diameter, as defined by the atom_style sphere -command. -

    -

    Per-particle polydispersity is not yet supported by this pair style; -per-type polydispersity is allowed. This means all particles of the -same type must have the same diameter. Each type can have a different -diameter. -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Safran) Safran, Statistical Thermodynamics of Surfaces, Interfaces, -And Membranes, Westview Press, ISBN: 978-0813340791 (2003). -

    - diff --git a/doc/doc2/pair_zbl.html b/doc/doc2/pair_zbl.html deleted file mode 100644 index aa2fa7f1ce..0000000000 --- a/doc/doc2/pair_zbl.html +++ /dev/null @@ -1,148 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    pair_style zbl command -

    -

    pair_style zbl/gpu command -

    -

    pair_style zbl/omp command -

    -

    Syntax: -

    -
    pair_style zbl inner outer 
-
    -
    • inner = distance where switching function begins -
    • outer = global cutoff for ZBL interaction -
    -

    Examples: -

    -
    pair_style zbl 3.0 4.0
-pair_coeff * * 73.0 73.0
-pair_coeff 1 1 14.0 14.0 
-
    -

    Description: -

    -

    Style zbl computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear -repulsion for describing high-energy collisions between atoms. -(Ziegler). It includes an additional switching function -that ramps the energy, force, and curvature smoothly to zero -between an inner and outer cutoff. The potential -energy due to a pair of atoms at a distance r_ij is given by: -

    -
    -
    -

    where e is the electron charge, epsilon_0 is the electrical -permittivity of vacuum, and Z_i and Z_j are the nuclear charges of the -two atoms. The switching function S(r) is identical to that used by -pair_style lj/gromacs. Here, the inner and outer -cutoff are the same for all pairs of atom types. -

    -

    The following coefficients must be defined for each pair of atom types -via the pair_coeff command as in the examples above, -or in the LAMMPS data file. -

    -
    • Z_i (atomic number for first atom type, e.g. 13.0 for aluminum) -
    -
    • Z_j (ditto for second atom type) -
    -

    The values of Z_i and Z_j are normally equal to the atomic -numbers of the two atom types. Thus, the user may optionally -specify only the coefficients for each I==I pair, and rely -on the obvious mixing rule for cross interactions (see below). -Note that when I==I it is required that Z_i == Z_j. When used -with hybrid/overlay and pairs are assigned -to more than one sub-style, the mixing rule is not used and -each pair of types interacting with the ZBL sub-style must -be included in a pair_coeff command. -

    -

    IMPORTANT NOTE: The numerical values of the exponential decay -constants in the screening function depend on the unit of distance. In -the above equation they are given for units of angstroms. LAMMPS will -automatically convert these values to the distance unit of the -specified LAMMPS units setting. The values of Z should -always be given as multiples of a proton's charge, e.g. 29.0 for -copper. -

    -
    - -

    Styles with a cuda, gpu, intel, kk, omp, or opt suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. -

    -

    These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, -KOKKOS, USER-OMP and OPT packages, respectively. They are only -enabled if LAMMPS was built with those packages. See the Making -LAMMPS section for more info. -

    -

    You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the -suffix command-line -switch when you invoke LAMMPS, or you can -use the suffix command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Mixing, shift, table, tail correction, restart, rRESPA info: -

    -

    For atom type pairs I,J and I != J, the Z_i and Z_j coefficients -can be mixed by taking Z_i and Z_j from the values specified for -I == I and J == J cases. When used -with hybrid/overlay and pairs are assigned -to more than one sub-style, the mixing rule is not used and -each pair of types interacting with the ZBL sub-style -must be included in a pair_coeff command. -The pair_modify mix option has no effect on -the mixing behavior -

    -

    The ZBL pair style does not support the pair_modify -shift option, since the ZBL interaction is already smoothed to 0.0 at -the cutoff. -

    -

    The pair_modify table option is not relevant for -this pair style. -

    -

    This pair style does not support the pair_modify -tail option for adding long-range tail corrections to energy and -pressure, since there are no corrections for a potential that goes to -0.0 at the cutoff. -

    -

    This pair style does not write information to binary restart -files, so pair_style and pair_coeff commands must be -specified in an input script that reads a restart file. -

    -

    This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

    -
    - -

    Restrictions: none -

    -

    Related commands: -

    -

    pair_coeff -

    -

    Default: none -

    -
    - - - -

    (Ziegler) J.F. Ziegler, J. P. Biersack and U. Littmark, "The -Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. -

    - diff --git a/doc/doc2/partition.html b/doc/doc2/partition.html deleted file mode 100644 index 4832823338..0000000000 --- a/doc/doc2/partition.html +++ /dev/null @@ -1,78 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    partition command -

    -

    Syntax: -

    -
    partition style N command ... 
-
    -
    • style = yes or no -
    • N = partition number (see asterisk form below) -
    • command = any LAMMPS command -
    -

    Examples: -

    -
    partition yes 1 processors 4 10 6
-partition no 5 print "Active partition"
-partition yes *5 fix all nve
-partition yes 6* fix all nvt temp 1.0 1.0 0.1 
-
    -

    Description: -

    -

    This command invokes the specified command on a subset of the -partitions of processors you have defined via the -partition -command-line switch. See Section_start 6 -for an explanation of the switch. -

    -

    Normally, every input script command in your script is invoked by -every partition. This behavior can be modified by defining world- or -universe-style variables that have different values -for each partition. This mechanism can be used to cause your script -to jump to different input script files on different partitions, if -such a variable is used in a jump command. -

    -

    The "partition" command is another mechanism for having as input -script operate differently on different partitions. It is basically a -prefix on any LAMMPS command. The commmand will only be invoked on -the partition(s) specified by the style and N arguments. -

    -

    If the style is yes, the command will be invoked on any partition -which matches the N argument. If the style is no the command -will be invoked on all the partitions which do not match the Np -argument. -

    -

    Partitions are numbered from 1 to Np, where Np is the number of -partitions specified by the -partition command-line -switch. -

    -

    N can be specified in one of two ways. An explicit numeric value -can be used, as in the 1st example above. Or a wild-card asterisk can -be used to span a range of partition numbers. This takes the form "*" -or "*n" or "n*" or "m*n". An asterisk with no numeric values means -all partitions from 1 to Np. A leading asterisk means all partitions -from 1 to n (inclusive). A trailing asterisk means all partitions -from n to Np (inclusive). A middle asterisk means all partitions from -m to n (inclusive). -

    -

    This command can be useful for the "run_style verlet/split" command -which imposed requirements on how the processors -command lays out a 3d grid of processors in each of 2 partitions. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    run_style verlet/split -

    -

    Default: none -

    - diff --git a/doc/doc2/prd.html b/doc/doc2/prd.html deleted file mode 100644 index 5c4c5ce49a..0000000000 --- a/doc/doc2/prd.html +++ /dev/null @@ -1,339 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    prd command -

    -

    Syntax: -

    -
    prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ... 
-
    -
    • N = # of timesteps to run (not including dephasing/quenching) - -
    • t_event = timestep interval between event checks - -
    • n_dephase = number of velocity randomizations to perform in each dephase run - -
    • t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase - -
    • t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated - -
    • compute-ID = ID of the compute used for event detection - -
    • random_seed = random # seed (positive integer) - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = min or temp or vel - -
        min values = etol ftol maxiter maxeval
-    etol = stopping tolerance for energy, used in quenching
-    ftol = stopping tolerance for force, used in quenching
-    maxiter = max iterations of minimize, used in quenching
-    maxeval = max number of force/energy evaluations, used in quenching
-  temp value = Tdephase
-    Tdephase = target temperature for velocity randomization, used in dephasing
-  vel values = loop dist
-    loop = all or local or geom, used in dephasing
-    dist = uniform or gaussian, used in dephasing
-  time value = steps or clock
-    steps = simulation runs for N timesteps on each replica (default)
-    clock = simulation runs for N timesteps across all replicas 
-
      - -
    -

    Examples: -

    -
    prd 5000 100 10 10 100 1 54982
-prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200 
-
    -

    Description: -

    -

    Run a parallel replica dynamics (PRD) simulation using multiple -replicas of a system. One or more replicas can be used. The total -number of steps N to run can be interpreted in one of two ways; see -discussion of the time keyword below. -

    -

    PRD is described in this paper by Art Voter. It is a method -for performing accelerated dynamics that is suitable for -infrequent-event systems that obey first-order kinetics. A good -overview of accelerated dynamics methods for such systems in given in -this review paper from the same group. To quote from the -paper: "The dynamical evolution is characterized by vibrational -excursions within a potential basin, punctuated by occasional -transitions between basins." The transition probability is -characterized by p(t) = k*exp(-kt) where k is the rate constant. -Running multiple replicas gives an effective enhancement in the -timescale spanned by the multiple simulations, while waiting for an -event to occur. -

    -

    Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the -partition command-line -switch; see Section_start 6 of the -manual. Note that if you have MPI installed, you can run a -multi-replica simulation with more replicas (partitions) than you have -physical processors, e.g you can run a 10-replica simulation on one or -two processors. For PRD, this makes little sense, since this offers -no effective parallel speed-up in searching for infrequent events. See -Section_howto 5 of the manual for further -discussion. -

    -

    When a PRD simulation is performed, it is assumed that each replica is -running the same model, though LAMMPS does not check for this. -I.e. the simulation domain, the number of atoms, the interaction -potentials, etc should be the same for every replica. -

    -

    A PRD run has several stages, which are repeated each time an "event" -occurs in one of the replicas, as defined below. The logic for a PRD -run is as follows: -

    -
    while (time remains):
-  dephase for n_dephase*t_dephase steps
-  until (event occurs on some replica):
-    run dynamics for t_event steps
-    quench
-    check for uncorrelated event on any replica
-  until (no correlated event occurs):
-    run dynamics for t_correlate steps
-    quench
-    check for correlated event on this replica
-  event replica shares state with all replicas 
-
    -

    Before this loop begins, the state of the system on replica 0 is -shared with all replicas, so that all replicas begin from the same -initial state. The first potential energy basin is identified by -quenching (an energy minimization, see below) the initial state and -storing the resulting coordinates for reference. -

    -

    In the first stage, dephasing is performed by each replica -independently to eliminate correlations between replicas. This is -done by choosing a random set of velocities, based on the -random_seed that is specified, and running t_dephase timesteps of -dynamics. This is repeated n_dephase times. At each of the -n_dephase stages, if an event occurs during the t_dephase steps of -dynamics for a particular replica, the replica repeats the stage until -no event occurs. -

    -

    If the temp keyword is not specified, the target temperature for -velocity randomization for each replica is the current temperature of -that replica. Otherwise, it is the specified Tdephase temperature. -The style of velocity randomization is controlled using the keyword -vel with arguments that have the same meaning as their counterparts -in the velocity command. -

    -

    In the second stage, each replica runs dynamics continuously, stopping -every t_event steps to check if a transition event has occurred. -This check is performed by quenching the system and comparing the -resulting atom coordinates to the coordinates from the previous basin. -The first time through the PRD loop, the "previous basin" is the set -of quenched coordinates from the initial state of the system. -

    -

    A quench is an energy minimization and is performed by whichever -algorithm has been defined by the min_style command. -Minimization parameters may be set via the -min_modify command and by the min keyword of the -PRD command. The latter are the settings that would be used with the -minimize command. Note that typically, you do not -need to perform a highly-converged minimization to detect a transition -event. -

    -

    The event check is performed by a compute with the specified -compute-ID. Currently there is only one compute that works with the -PRD commmand, which is the compute -event/displace command. Other -event-checking computes may be added. Compute -event/displace checks whether any atom in -the compute group has moved further than a specified threshold -distance. If so, an "event" has occurred. -

    -

    In the third stage, the replica on which the event occurred (event -replica) continues to run dynamics to search for correlated events. -This is done by running dynamics for t_correlate steps, quenching -every t_event steps, and checking if another event has occurred. -

    -

    The first time no correlated event occurs, the final state of the -event replica is shared with all replicas, the new basin reference -coordinates are updated with the quenched state, and the outer loop -begins again. While the replica event is searching for correlated -events, all the other replicas also run dynamics and event checking -with the same schedule, but the final states are always overwritten by -the state of the event replica. -

    -

    The outer loop of the pseudo-code above continues until N steps of -dynamics have been performed. Note that N only includes the -dynamics of stages 2 and 3, not the steps taken during dephasing or -the minimization iterations of quenching. The specified N is -interpreted in one of two ways, depending on the time keyword. If -the time value is steps, which is the default, then each replica -runs for N timesteps. If the time value is clock, then the -simulation runs until N aggregate timesteps across all replicas have -elapsed. This aggregate time is the "clock" time defined below, which -typically advances nearly M times faster than the timestepping on a -single replica. -

    -
    - -

    Four kinds of output can be generated during a PRD run: event -statistics, thermodynamic output by each replica, dump files, and -restart files. -

    -

    When running with multiple partitions (each of which is a replica in -this case), the print-out to the screen and master log.lammps file is -limited to event statistics. Note that if a PRD run is performed on -only a single replica then the event statistics will be intermixed -with the usual thermodynamic output discussed below. -

    -

    The quantities printed each time an event occurs are the timestep, CPU -time, clock, event number, a correlation flag, the number of -coincident events, and the replica number of the chosen event. -

    -

    The timestep is the usual LAMMPS timestep, except that time does not -advance during dephasing or quenches, but only during dynamics. Note -that are two kinds of dynamics in the PRD loop listed above. The -first is when all replicas are performing independent dynamics, -waiting for an event to occur. The second is when correlated events -are being searched for and only one replica is running dynamics. -

    -

    The CPU time is the total processor time since the start of the PRD -run. -

    -

    The clock is the same as the timestep except that it advances by M -steps every timestep during the first kind of dynamics when the M -replicas are running independently. The clock advances by only 1 step -per timestep during the second kind of dynamics, since only a single -replica is checking for a correlated event. Thus "clock" time -represents the aggregate time (in steps) that effectively elapses -during a PRD simulation on M replicas. If most of the PRD run is -spent in the second stage of the loop above, searching for infrequent -events, then the clock will advance nearly M times faster than it -would if a single replica was running. Note the clock time between -events will be drawn from p(t). -

    -

    The event number is a counter that increments with each event, whether -it is uncorrelated or correlated. -

    -

    The correlation flag will be 0 when an uncorrelated event occurs -during the second stage of the loop listed above, i.e. when all -replicas are running independently. The correlation flag will be 1 -when a correlated event occurs during the third stage of the loop -listed above, i.e. when only one replica is running dynamics. -

    -

    When more than one replica detects an event at the end of the second -stage, then one of them is chosen at random. The number of coincident -events is the number of replicas that detected an event. Normally, we -expect this value to be 1. If it is often greater than 1, then either -the number of replicas is too large, or t_event is too large. -

    -

    The replica number is the ID of the replica (from 0 to M-1) that -found the event. -

    -
    - -

    When running on multiple partitions, LAMMPS produces additional log -files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For -the PRD command, these contain the thermodynamic output for each -replica. You will see short runs and minimizations corresponding to -the dynamics and quench operations of the loop listed above. The -timestep will be reset aprpopriately depending on whether the -operation advances time or not. -

    -

    After the PRD command completes, timing statistics for the PRD run are -printed in each replica's log file, giving a breakdown of how much CPU -time was spent in each stage (dephasing, dynamics, quenching, etc). -

    -
    - -

    Any dump files defined in the input script, will be -written to during a PRD run at timesteps corresponding to both -uncorrelated and correlated events. This means the the requested dump -frequency in the dump command is ignored. There will be -one dump file (per dump command) created for all partitions. -

    -

    The atom coordinates of the dump snapshot are those of the minimum -energy configuration resulting from quenching following a transition -event. The timesteps written into the dump files correspond to the -timestep at which the event occurred and NOT the clock. A dump -snapshot corresponding to the initial minimum state used for event -detection is written to the dump file at the beginning of each PRD -run. -

    -
    - -

    If the restart command is used, a single restart file -for all the partitions is generated, which allows a PRD run to be -continued by a new input script in the usual manner. -

    -

    The restart file is generated at the end of the loop listed above. If -no correlated events are found, this means it contains a snapshot of -the system at time T + t_correlate, where T is the time at which the -uncorrelated event occurred. If correlated events were found, then it -contains a snapshot of the system at time T + t_correlate, where T -is the time of the last correlated event. -

    -

    The restart frequency specified in the restart command -is interpreted differently when performing a PRD run. It does not -mean the timestep interval between restart files. Instead it means an -event interval for uncorrelated events. Thus a frequency of 1 means -write a restart file every time an uncorrelated event occurs. A -frequency of 10 means write a restart file every 10th uncorrelated -event. -

    -

    When an input script reads a restart file from a previous PRD run, the -new script can be run on a different number of replicas or processors. -However, it is assumed that t_correlate in the new PRD command is -the same as it was previously. If not, the calculation of the "clock" -value for the first event in the new run will be slightly off. -

    -
    - -

    Restrictions: -

    -

    This command can only be used if LAMMPS was built with the REPLICA -package. See the Making LAMMPS section -for more info on packages. -

    -

    N and t_correlate settings must be integer multiples of -t_event. -

    -

    Runs restarted from restart file written during a PRD run will not -produce identical results due to changes in the random numbers used -for dephasing. -

    -

    This command cannot be used when any fixes are defined that keep track -of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as fix -ave/spatial. Also fix -dt/reset and fix deposit. -

    -

    Related commands: -

    -

    compute event/displace, -min_modify, min_style, -run_style, minimize, -velocity, temper, neb, -tad -

    -

    Default: -

    -

    The option defaults are min = 0.1 0.1 40 50, no temp setting, vel = -geom gaussian, and time = steps. -

    -
    - - - -

    (Voter) Voter, Phys Rev B, 57, 13985 (1998). -

    - - -

    (Voter2) Voter, Montalenti, Germann, Annual Review of Materials -Research 32, 321 (2002). -

    - diff --git a/doc/doc2/print.html b/doc/doc2/print.html deleted file mode 100644 index e97b5e2188..0000000000 --- a/doc/doc2/print.html +++ /dev/null @@ -1,86 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    print command -

    -

    Syntax: -

    -
    print string keyword value 
-
    -
    • string = text string to print, which may contain variables - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = file or append or screen - -
        file value = filename
-  append value = filename
-  screen value = yes or no 
-
      - -
    -

    Examples: -

    -
    print "Done with equilibration" file info.dat
-print Vol=$v append info.dat screen no
-print "The system volume is now $v" 
-print 'The system volume is now $v'
-print """
-System volume = $v
-System temperature = $t
-""" 
-
    -

    Description: -

    -

    Print a text string to the screen and logfile. The text string must -be a single argument, so if it is one line but more than one word, it -should be enclosed in single or double quotes. To generate multiple -lines of output, the string can be enclosed in triple quotes, as in -the last example above. If the text string contains variables, they -will be evaluated and their current values printed. -

    -

    If the file or append keyword is used, a filename is specified to -which the output will be written. If file is used, then the -filename is overwritten if it already exists. If append is used, -then the filename is appended to if it already exists, or created if -it does not exist. -

    -

    If the screen keyword is used, output to the screen and logfile can -be turned on or off as desired. -

    -

    If you want the print command to be executed multiple times (with -changing variable values), there are 3 options. First, consider using -the fix print command, which will print a string -periodically during a simulation. Second, the print command can be -used as an argument to the every option of the run -command. Third, the print command could appear in a section of the -input script that is looped over (see the jump and -next commands). -

    -

    See the variable command for a description of equal -style variables which are typically the most useful ones to use with -the print command. Equal-style variables can calculate formulas -involving mathematical operations, atom properties, group properties, -thermodynamic properties, global values calculated by a -compute or fix, or references to other -variables. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix print, variable -

    -

    Default: -

    -

    The option defaults are no file output and screen = yes. -

    - diff --git a/doc/doc2/processors.html b/doc/doc2/processors.html deleted file mode 100644 index d819aa4fb9..0000000000 --- a/doc/doc2/processors.html +++ /dev/null @@ -1,351 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    processors command -

    -

    Syntax: -

    -
    processors Px Py Pz keyword args ... 
-
    -
    • Px,Py,Pz = # of processors in each dimension of 3d grid overlaying the simulation domain - -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = grid or map or part or file - -
        grid arg = gstyle params ...
-    gstyle = onelevel or twolevel or numa or custom
-      onelevel params = none
-      twolevel params = Nc Cx Cy Cz
-        Nc = number of cores per node
-        Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
-      numa params = none
-      custom params = infile
-        infile = file containing grid layout
-  map arg = cart or cart/reorder or xyz or xzy or yxz or yzx or zxy or zyx
-     cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
-     cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
-     xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering
-  numa arg = none
-  part args = Psend Precv cstyle
-    Psend = partition # (1 to Np) which will send its processor layout
-    Precv = partition # (1 to Np) which will recv the processor layout
-    cstyle = multiple
-      multiple = Psend grid will be multiple of Precv grid in each dimension
-  file arg = outfile
-    outfile = name of file to write 3d grid of processors to 
-
      - -
    -

    Examples: -

    -
    processors * * 5 
-processors 2 4 4
-processors * * 8 map xyz
-processors * * * grid numa
-processors * * * grid twolevel 4 * * 1
-processors 4 8 16 grid custom myfile
-processors * * * part 1 2 multiple 
-
    -

    Description: -

    -

    Specify how processors are mapped as a regular 3d grid to the global -simulation box. The mapping involves 2 steps. First if there are P -processors it means choosing a factorization P = Px by Py by Pz so -that there are Px processors in the x dimension, and similarly for the -y and z dimensions. Second, the P processors are mapped to the -regular 3d grid. The arguments to this command control each of these -2 steps. -

    -

    The Px, Py, Pz parameters affect the factorization. Any of the 3 -parameters can be specified with an asterisk "*", which means LAMMPS -will choose the number of processors in that dimension of the grid. -It will do this based on the size and shape of the global simulation -box so as to minimize the surface-to-volume ratio of each processor's -sub-domain. -

    -

    Choosing explicit values for Px or Py or Pz can be used to override -the default manner in which LAMMPS will create the regular 3d grid of -processors, if it is known to be sub-optimal for a particular problem. -E.g. a problem where the extent of atoms will change dramatically in a -particular dimension over the course of the simulation. -

    -

    The product of Px, Py, Pz must equal P, the total # of processors -LAMMPS is running on. For a 2d simulation, Pz must -equal 1. -

    -

    Note that if you run on a prime number of processors P, then a grid -such as 1 x P x 1 will be required, which may incur extra -communication costs due to the high surface area of each processor's -sub-domain. -

    -

    Also note that if multiple partitions are being used then P is the -number of processors in this partition; see this -section for an explanation of the --partition command-line switch. Also note that you can prefix the -processors command with the partition command to -easily specify different Px,Py,Pz values for different partitions. -

    -

    You can use the partition command to specify -different processor grids for different partitions, e.g. -

    -
    partition yes 1 processors 4 4 4
-partition yes 2 processors 2 3 2 
-
    -

    IMPORTANT NOTE: This command only affects the initial regular 3d grid -created when the simulation box is first specified via a -create_box or read_data or -read_restart command. Or if the simulation box is -re-created via the replicate command. The same -regular grid is initially created, regardless of which -comm_style command is in effect. -

    -

    If load-balancing is never invoked via the balance or -fix balance commands, then the initial regular grid -will persist for all simulations. If balancing is performed, some of -the methods invoked by those commands retain the logical toplogy of -the initial 3d grid, and the mapping of processors to the grid -specified by the processors command. However the grid spacings in -different dimensions may change, so that processors own sub-domains of -different sizes. If the comm_style tiled command is -used, methods invoked by the balancing commands may discard the 3d -grid of processors and tile the simulation domain with sub-domains of -different sizes and shapes which no longer have a logical 3d -connectivity. If that occurs, all the information specified by the -processors command is ignored. -

    -
    - -

    The grid keyword affects the factorization of P into Px,Py,Pz and it -can also affect how the P processor IDs are mapped to the 3d grid of -processors. -

    -

    The onelevel style creates a 3d grid that is compatible with the -Px,Py,Pz settings, and which minimizes the surface-to-volume ratio of -each processor's sub-domain, as described above. The mapping of -processors to the grid is determined by the map keyword setting. -

    -

    The twolevel style can be used on machines with multicore nodes to -minimize off-node communication. It insures that contiguous -sub-sections of the 3d grid are assigned to all the cores of a node. -For example if Nc is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of -the 3d grid will correspond to the cores of each node. This affects -both the factorization and mapping steps. -

    -

    The Cx, Cy, Cz settings are similar to the Px, Py, Pz -settings, only their product should equal Nc. Any of the 3 -parameters can be specified with an asterisk "*", which means LAMMPS -will choose the number of cores in that dimension of the node's -sub-grid. As with Px,Py,Pz, it will do this based on the size and -shape of the global simulation box so as to minimize the -surface-to-volume ratio of each processor's sub-domain. -

    -

    IMPORTANT NOTE: For the twolevel style to work correctly, it -assumes the MPI ranks of processors LAMMPS is running on are ordered -by core and then by node. E.g. if you are running on 2 quad-core -nodes, for a total of 8 processors, then it assumes processors 0,1,2,3 -are on node 1, and processors 4,5,6,7 are on node 2. This is the -default rank ordering for most MPI implementations, but some MPIs -provide options for this ordering, e.g. via environment variable -settings. -

    -

    The numa style operates similar to the twolevel keyword except -that it auto-detects which cores are running on which nodes. -Currently, it does this in only 2 levels, but it may be extended in -the future to account for socket topology and other non-uniform memory -access (NUMA) costs. It also uses a different algorithm than the -twolevel keyword for doing the two-level factorization of the -simulation box into a 3d processor grid to minimize off-node -communication, and it does its own MPI-based mapping of nodes and -cores to the regular 3d grid. Thus it may produce a different layout -of the processors than the twolevel options. -

    -

    The numa style will give an error if the number of MPI processes is -not divisible by the number of cores used per node, or any of the Px -or Py of Pz values is greater than 1. -

    -

    IMPORTANT NOTE: Unlike the twolevel style, the numa style does not -require any particular ordering of MPI ranks i norder to work -correctly. This is because it auto-detects which processes are -running on which nodes. -

    -

    The custom style uses the file infile to define both the 3d -factorization and the mapping of processors to the grid. -

    -

    The file should have the following format. Any number of initial -blank or comment lines (starting with a "#" character) can be present. -The first non-blank, non-comment line should have -3 values: -

    -
    Px Py Py 
-
    -

    These must be compatible with the total number of processors -and the Px, Py, Pz settings of the processors commmand. -

    -

    This line should be immediately followed by -P = Px*Py*Pz lines of the form: -

    -
    ID I J K 
-
    -

    where ID is a processor ID (from 0 to P-1) and I,J,K are the -processors location in the 3d grid. I must be a number from 1 to Px -(inclusive) and similarly for J and K. The P lines can be listed in -any order, but no processor ID should appear more than once. -

    -
    - -

    The map keyword affects how the P processor IDs (from 0 to P-1) are -mapped to the 3d grid of processors. It is only used by the -onelevel and twolevel grid settings. -

    -

    The cart style uses the family of MPI Cartesian functions to perform -the mapping, namely MPI_Cart_create(), MPI_Cart_get(), -MPI_Cart_shift(), and MPI_Cart_rank(). It invokes the -MPI_Cart_create() function with its reorder flag = 0, so that MPI is -not free to reorder the processors. -

    -

    The cart/reorder style does the same thing as the cart style -except it sets the reorder flag to 1, so that MPI can reorder -processors if it desires. -

    -

    The xyz, xzy, yxz, yzx, zxy, and zyx styles are all -similar. If the style is IJK, then it maps the P processors to the -grid so that the processor ID in the I direction varies fastest, the -processor ID in the J direction varies next fastest, and the processor -ID in the K direction varies slowest. For example, if you select -style xyz and you have a 2x2x2 grid of 8 processors, the assignments -of the 8 octants of the simulation domain will be: -

    -
    proc 0 = lo x, lo y, lo z octant
-proc 1 = hi x, lo y, lo z octant
-proc 2 = lo x, hi y, lo z octant
-proc 3 = hi x, hi y, lo z octant
-proc 4 = lo x, lo y, hi z octant
-proc 5 = hi x, lo y, hi z octant
-proc 6 = lo x, hi y, hi z octant
-proc 7 = hi x, hi y, hi z octant 
-
    -

    Note that, in principle, an MPI implementation on a particular machine -should be aware of both the machine's network topology and the -specific subset of processors and nodes that were assigned to your -simulation. Thus its MPI_Cart calls can optimize the assignment of -MPI processes to the 3d grid to minimize communication costs. In -practice, however, few if any MPI implementations actually do this. -So it is likely that the cart and cart/reorder styles simply give -the same result as one of the IJK styles. -

    -

    Also note, that for the twolevel grid style, the map setting is -used to first map the nodes to the 3d grid, then again to the cores -within each node. For the latter step, the cart and cart/reorder -styles are not supported, so an xyz style is used in their place. -

    -
    - -

    The part keyword affects the factorization of P into Px,Py,Pz. -

    -

    It can be useful when running in multi-partition mode, e.g. with the -run_style verlet/split command. It specifies a -dependency bewteen a sending partition Psend and a receiving -partition Precv which is enforced when each is setting up their own -mapping of their processors to the simulation box. Each of Psend -and Precv must be integers from 1 to Np, where Np is the number of -partitions you have defined via the -partition command-line -switch. -

    -

    A "dependency" means that the sending partition will create its -regular 3d grid as Px by Py by Pz and after it has done this, it will -send the Px,Py,Pz values to the receiving partition. The receiving -partition will wait to receive these values before creating its own -regular 3d grid and will use the sender's Px,Py,Pz values as a -constraint. The nature of the constraint is determined by the -cstyle argument. -

    -

    For a cstyle of multiple, each dimension of the sender's processor -grid is required to be an integer multiple of the corresponding -dimension in the receiver's processor grid. This is a requirement of -the run_style verlet/split command. -

    -

    For example, assume the sending partition creates a 4x6x10 grid = 240 -processor grid. If the receiving partition is running on 80 -processors, it could create a 4x2x10 grid, but it will not create a -2x4x10 grid, since in the y-dimension, 6 is not an integer multiple of -4. -

    -

    IMPORTANT NOTE: If you use the partition command to -invoke different "processsors" commands on different partitions, and -you also use the part keyword, then you must insure that both the -sending and receiving partitions invoke the "processors" command that -connects the 2 partitions via the part keyword. LAMMPS cannot -easily check for this, but your simulation will likely hang in its -setup phase if this error has been made. -

    -
    - -

    The file keyword writes the mapping of the factorization of P -processors and their mapping to the 3d grid to the specified file -outfile. This is useful to check that you assigned physical -processors in the manner you desired, which can be tricky to figure -out, especially when running on multiple partitions or on, a multicore -machine or when the processor ranks were reordered by use of the --reorder command-line switch or due to -use of MPI-specific launch options such as a config file. -

    -

    If you have multiple partitions you should insure that each one writes -to a different file, e.g. using a world-style variable -for the filename. The file has a self-explanatory header, followed by -one-line per processor in this format: -

    -

    world-ID universe-ID original-ID: I J K: name -

    -

    The IDs are the processor's rank in this simulation (the world), the -universe (of multiple simulations), and the original MPI communicator -used to instantiate LAMMPS, respectively. The world and universe IDs -will only be different if you are running on more than one partition; -see the -partition command-line switch. -The universe and original IDs will only be different if you used the --reorder command-line switch to reorder -the processors differently than their rank in the original -communicator LAMMPS was instantiated with. -

    -

    I,J,K are the indices of the processor in the regular 3d grid, each -from 1 to Nd, where Nd is the number of processors in that dimension -of the grid. -

    -

    The name is what is returned by a call to MPI_Get_processor_name() -and should represent an identifier relevant to the physical processors -in your machine. Note that depending on the MPI implementation, -multiple cores can have the same name. -

    -
    - -

    Restrictions: -

    -

    This command cannot be used after the simulation box is defined by a -read_data or create_box command. -It can be used before a restart file is read to change the 3d -processor grid from what is specified in the restart file. -

    -

    The grid numa keyword only currently works with the map cart -option. -

    -

    The part keyword (for the receiving partition) only works with the -grid onelevel or grid twolevel options. -

    -

    Related commands: -

    -

    partition, -reorder command-line switch -

    -

    Default: -

    -

    The option defaults are Px Py Pz = * * *, grid = onelevel, and map = -cart. -

    - diff --git a/doc/doc2/python.html b/doc/doc2/python.html deleted file mode 100644 index 9d0aa9868e..0000000000 --- a/doc/doc2/python.html +++ /dev/null @@ -1,490 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    python command -

    -

    Syntax: -

    -
    python func keyword args ... 
-
    -
    • func = name of Python function - -
    • one or more keyword/args pairs must be appended - -
      keyword = invoke or input or return or format or file or here or exists
-  invoke arg = none = invoke the previously defined Python function
-  input args = N i1 i2 ... iN
-    N = # of inputs to function
-    i1,...,iN = value, SELF, or LAMMPS variable name
-      value = integer number, floating point number, or string
-      SELF = reference to LAMMPS itself which can be accessed by Python function
-      variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
-  return arg = varReturn
-    varReturn = v_name  = LAMMPS variable name which return value of function will be assigned to
-  format arg = fstring with M characters 
-    M = N if no return value, where N = # of inputs
-    M = N+1 if there is a return value
-    fstring = each character (i,f,s,p) corresponds in order to an input or return value
-    'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
-  file arg = filename
-    filename = file of Python code, which defines func
-  here arg = inline
-    inline = one or more lines of Python code which defines func
-             must be a single argument, typically enclosed between triple quotes
-  exists arg = none = Python code has been loaded by previous python command 
-
      - -
    -

    Examples: -

    -
    python pForce input 2 v_x 20.0 return v_f format fff file force.py
-python pForce invoke 
-
    -
    python factorial input 1 myN return v_fac format ii here """
-def factorial(n):
-  if n == 1: return n
-  return n * factorial(n-1)
- """ 
-
    -
    python loop input 1 SELF return v_value format -f here """
-def loop(lmpptr,N,cut0):
-  from lammps import lammps
-  lmp = lammps(ptr=lmpptr) 
-
    -
      # loop N times, increasing cutoff each time 
-
    -
      for i in range(N):
-    cut = cut0 + i*0.1
-    lmp.set_variable("cut",cut)               # set a variable in LAMMPS
-    lmp.command("pair_style lj/cut ${cut}")   # LAMMPS commands
-    lmp.command("pair_coeff * * 1.0 1.0")
-    lmp.command("run 100")
- """ 
-
    -

    Description: -

    -

    IMPORTANT NOTE: It is not currently possible to use the -python command described in this section with Python 3, -only with Python 2. The C API changed from Python 2 to 3 and the -LAMMPS code is not compatible with both. -

    -

    Define a Python function or execute a previously defined function. -Arguments, including LAMMPS variables, can be passed to the function -from the LAMMPS input script and a value returned by the Python -function to a LAMMPS variable. The Python code for the function can -be included directly in the input script or in a separate Python file. -The function can be standard Python code or it can make "callbacks" to -LAMMPS through its library interface to query or set internal values -within LAMMPS. This is a powerful mechanism for performing complex -operations in a LAMMPS input script that are not possible with the -simple input script and variable syntax which LAMMPS defines. Thus -your input script can operate more like a true programming language. -

    -

    Use of this command requires building LAMMPS with the PYTHON package -which links to the Python library so that the Python interpreter is -embedded in LAMMPS. More details about this process are given below. -

    -

    There are two ways to invoke a Python function once it has been -defined. One is using the invoke keyword. The other is to assign -the function to a python-style variable defined in -your input script. Whenever the variable is evaluated, it will -execute the Python function to assign a value to the variable. Note -that variables can be evaluated in many different ways within LAMMPS. -They can be substituted for directly in an input script. Or they can -be passed to various commands as arguments, so that the variable is -evaluated during a simulation run. -

    -

    A broader overview of how Python can be used with LAMMPS is -given in Section python. There is an -examples/python directory which illustrates use of the python -command. -

    -
    - -

    The func setting specifies the name of the Python function. The -code for the function is defined using the file or here keywords -as explained below. -

    -

    If the invoke keyword is used, no other keywords can be used, and a -previous python command must have defined the Python function -referenced by this command. This invokes the Python function with the -previously defined arguments and return value processed as explained -below. You can invoke the function as many times as you wish in your -input script. -

    -

    The input keyword defines how many arguments N the Python function -expects. If it takes no arguments, then the input keyword should -not be used. Each argument can be specified directly as a value, -e.g. 6 or 3.14159 or abc (a string of characters). The type of each -argument is specified by the format keyword as explained below, so -that Python will know how to interpret the value. If the word SELF is -used for an argument it has a special meaning. A pointer is passed to -the Python function which it converts into a reference to LAMMPS -itself. This enables the function to call back to LAMMPS through its -library interface as explained below. This allows the Python function -to query or set values internal to LAMMPS which can affect the -subsequent execution of the input script. A LAMMPS variable can also -be used as an argument, specified as v_name, where "name" is the name -of the variable. Any style of LAMMPS variable can be used, as defined -by the variable command. Each time the Python -function is invoked, the LAMMPS variable is evaluated and its value is -passed to the Python function. -

    -

    The return keyword is only needed if the Python function returns a -value. The specified varReturn must be of the form v_name, where -"name" is the name of a python-style LAMMPS variable, defined by the -variable command. The Python function can return a -numeric or string value, as specified by the format keyword. -

    -

    As explained on the variable doc page, the definition -of a python-style variable associates a Python function name with the -variable. This must match the func setting for this command. For -exampe these two commands would be self-consistent: -

    -
    variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py 
-
    -

    The two commands can appear in either order in the input script so -long as both are specified before the Python function is invoked for -the first time. -

    -

    The format keyword must be used if the input or return keyword -is used. It defines an fstring with M characters, where M = sum of -number of inputs and outputs. The order of characters corresponds to -the N inputs, followed by the return value (if it exists). Each -character must be one of the following: "i" for integer, "f" for -floating point, "s" for string, or "p" for SELF. Each character -defines the type of the corresponding input or output value of the -Python function and affects the type conversion that is performed -internally as data is passed back and forth between LAMMPS and Python. -Note that it is permissible to use a python-style -variable in a LAMMPS command that allows for an -equal-style variable as an argument, but only if the output of the -Python function is flagged as a numeric value ("i" or "f") via the -format keyword. -

    -

    Either the file, here, or exists keyword must be used, but only -one of them. These keywords specify what Python code to load into the -Python interpreter. The file keyword gives the name of a file, -which should end with a ".py" suffix, which contains Python code. The -code will be immediately loaded into and run in the "main" module of -the Python interpreter. Note that Python code which contains a -function definition does not "execute" the function when it is run; it -simply defines the function so that it can be invoked later. -

    -

    The here keyword does the same thing, except that the Python code -follows as a single argument to the here keyword. This can be done -using triple quotes as delimiters, as in the examples above. This -allows Python code to be listed verbatim in your input script, with -proper indentation, blank lines, and comments, as desired. See -Section 3.2, for an explanation of how -triple quotes can be used as part of input script syntax. -

    -

    The exists keyword takes no argument. It means that Python code -containing the required Python function defined by the func setting, -is assumed to have been previously loaded by another python command. -

    -

    Note that the Python code that is loaded and run must contain a -function with the specified func name. To operate properly when -later invoked, the the function code must match the input and -return and format keywords specified by the python command. -Otherwise Python will generate an error. -

    -
    - -

    This section describes how Python code can be written to work with -LAMMPS. -

    -

    Whether you load Python code from a file or directly from your input -script, via the file and here keywords, the code can be identical. -It must be indented properly as Python requires. It can contain -comments or blank lines. If the code is in your input script, it -cannot however contain triple-quoted Python strings, since that will -conflict with the triple-quote parsing that the LAMMPS input script -performs. -

    -

    All the Python code you specify via one or more python commands is -loaded into the Python "main" module, i.e. __main__. The code can -define global variables or statements that are outside of function -definitions. It can contain multiple functions, only one of which -matches the func setting in the python command. This means you can -use the file keyword once to load several functions, and the -exists keyword thereafter in subsequent python commands to access -the other functions previously loaded. -

    -

    A Python function you define (or more generally, the code you load) -can import other Python modules or classes, it can make calls to other -system functions or functions you define, and it can access or modify -global variables (in the "main" module) which will persist between -successive function calls. The latter can be useful, for example, to -prevent a function from being invoke multiple times per timestep by -different commands in a LAMMPS input script that access the returned -python-style variable associated with the function. For example, -consider this function loaded with two global variables defined -outside the function: -

    -
    nsteplast = -1
-nvaluelast = 0 
-
    -
    def expensive(nstep):
-  global nsteplast,nvaluelast
-  if nstep == nsteplast: return nvaluelast
-  nsteplast = nstep  
-  # perform complicated calculation
-  nvalue = ...
-  nvaluelast = nvalue
-  return nvalue 
-
    -

    Nsteplast stores the previous timestep the function was invoked -(passed as an argument to the function). Nvaluelast stores the return -value computed on the last function invocation. If the function is -invoked again on the same timestep, the previous value is simply -returned, without re-computing it. The "global" statement inside the -Python function allows it to overwrite the global variables. -

    -

    Note that if you load Python code multiple times (via multiple python -commands), you can overwrite previously loaded variables and functions -if you are not careful. E.g. if the code above were loaded twice, the -global variables would be re-initialized, which might not be what you -want. Likewise, if a function with the same name exists in two chunks -of Python code you load, the function loaded second will override the -function loaded first. -

    -

    It's important to realize that if you are running LAMMPS in parallel, -each MPI task will load the Python interpreter and execute a local -copy of the Python function(s) you define. There is no connection -between the Python interpreters running on different processors. -This implies three important things. -

    -

    First, if you put a print statement in your Python function, you will -see P copies of the output, when running on P processors. If the -prints occur at (nearly) the same time, the P copies of the output may -be mixed together. Welcome to the world of parallel programming and -debugging. -

    -

    Second, if your Python code loads modules that are not pre-loaded by -the Python library, then it will load the module from disk. This may -be a bottleneck if 1000s of processors try to load a module at the -same time. On some large supercomputers, loading of modules from disk -by Python may be disabled. In this case you would need to pre-build a -Python library that has the required modules pre-loaded and link -LAMMPS with that library. -

    -

    Third, if your Python code calls back to LAMMPS (discussed in the -next section) and causes LAMMPS to perform an MPI operation requires -global communication (e.g. via MPI_Allreduce), such as computing the -global temperature of the system, then you must insure all your Python -functions (running independently on different processors) call back to -LAMMPS. Otherwise the code may hang. -

    -
    - -

    Your Python function can "call back" to LAMMPS through its -library interface, if you use the SELF input to pass Python -a pointer to LAMMPS. The mechanism for doing this in your -Python function is as follows: -

    -
    def foo(lmpptr,...):
-  from lammps import lammps
-  lmp = lammps(ptr=lmpptr)
-  lmp.command('print "Hello from inside Python"')
-  ... 
-
    -

    The function definition must include a variable (lmpptr in this case) -which corresponds to SELF in the python command. The first line of -the function imports the Python module lammps.py in the python dir of -the distribution. The second line creates a Python object "lmp" which -wraps the instance of LAMMPS that called the function. The -"ptr=lmpptr" argument is what makes that happen. The thrid line -invokes the command() function in the LAMMPS library interface. It -takes a single string argument which is a LAMMPS input script command -for LAMMPS to execute, the same as if it appeared in your input -script. In this case, LAMMPS should output -

    -
    Hello from inside Python 
-
    -

    to the screen and log file. Note that since the LAMMPS print command -itself takes a string in quotes as its argument, the Python string -must be delimited with a different style of quotes. -

    -

    Section 11.7 describes the syntax for how -Python wraps the various functions included in the LAMMPS library -interface. -

    -

    A more interesting example is in the examples/python/in.python script -which loads and runs the following function from examples/python/funcs.py: -

    -
    def loop(N,cut0,thresh,lmpptr):
-  print "LOOP ARGS",N,cut0,thresh,lmpptr
-  from lammps import lammps
-  lmp = lammps(ptr=lmpptr)
-  natoms = lmp.get_natoms() 
-
    -
      for i in range(N):
-    cut = cut0 + i*0.1 
-
    -
        lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
-    lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
-    #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option 
-
    -
        lmp.command("pair_coeff * * 1.0 1.0")       # ditto
-    lmp.command("run 10")                       # ditto
-    pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
-    print "PE",pe/natoms,thresh
-    if pe/natoms < thresh: return 
-
    -

    with these input script commands: -

    -
    python          loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
-python          loop invoke 
-
    -

    This has the effect of looping over a series of 10 short runs (10 -timesteps each) where the pair style cutoff is increased from a value -of 1.0 in distance units, in increments of 0.1. The looping stops -when the per-atom potential energy falls below a threshhold of -4.0 in -energy units. More generally, Python can be used to implement a loop -with complex logic, much more so than can be created using the LAMMPS -jump and if commands. -

    -

    Several LAMMPS library functions are called from the loop function. -Get_natoms() returns the number of atoms in the simulation, so that it -can be used to normalize the potential energy that is returned by -extract_compute() for the "thermo_pe" compute that is defined by -default for LAMMPS thermodynamic output. Set_variable() sets the -value of a string variable defined in LAMMPS. This library function -is a useful way for a Python function to return multiple values to -LAMMPS, more than the single value that can be passed back via a -return statement. This cutoff value in the "cut" variable is then -substituted (by LAMMPS) in the pair_style command that is executed -next. Alternatively, the "LAMMPS command option" line could be used -in place of the 2 preceeding lines, to have Python insert the value -into the LAMMPS command string. -

    -

    IMPORTANT NOTE: When using the callback mechanism just described, -recognize that there are some operations you should not attempt -because LAMMPS cannot execute them correctly. If the Python function -is invoked between runs in the LAMMPS input script, then it should be -OK to invoke any LAMMPS input script command via the library interface -command() or file() functions, so long as the command would work if it -were executed in the LAMMPS input script directly at the same point. -

    -

    However, a Python function can also be invoked during a run, whenever -an associated LAMMPS variable it is assigned to is evaluted. If the -variable is an input argument to another LAMMPS command (e.g. fix -setforce), then the Python function will be invoked -inside the class for that command, in one of its methods that is -invoked in the middle of a timestep. You cannot execute arbitrary -input script commands from the Python function (again, via the -command() or file() functions) at that point in the run and expect it -to work. Other library functions such as those that invoke computes -or other variables may have hidden side effects as well. In these -cases, LAMMPS has no simple way to check that something illogical is -being attempted. -

    -
    - -

    If you run Python code directly on your workstation, either -interactively or by using Python to launch a Python script stored in a -file, and your code has an error, you will typically see informative -error messages. That is not the case when you run Python code from -LAMMPS using an embedded Python interpreter. The code will typically -fail silently. LAMMPS will catch some errors but cannot tell you -where in the Python code the problem occurred. For example, if the -Python code cannot be loaded and run because it has syntax or other -logic errors, you may get an error from Python pointing to the -offending line, or you may get one of these generic errors from -LAMMPS: -

    -
    Could not process Python file
-Could not process Python string 
-
    -

    When the Python function is invoked, if it does not return properly, -you will typically get this generic error from LAMMPS: -

    -
    Python function evaluation failed 
-
    -

    Here are three suggestions for debugging your Python code while -running it under LAMMPS. -

    -

    First, don't run it under LAMMPS, at least to start with! Debug it -using plain Python. Load and invoke your function, pass it arguments, -check return values, etc. -

    -

    Second, add Python print statements to the function to check how far -it gets and intermediate values it calculates. See the discussion -above about printing from Python when running in parallel. -

    -

    Third, use Python exception handling. For example, say this statement -in your Python function is failing, because you have not initialized the -variable foo: -

    -
    foo += 1 
-
    -

    If you put one (or more) statements inside a "try" statement, -like this: -

    -
    import exceptions
-print "Inside simple function"
-try:
-  foo += 1      # one or more statements here
-except Exception, e:
-  print "FOO error:",e 
-
    -

    then you will get this message printed to the screen: -

    -
    FOO error: local variable 'foo' referenced before assignment 
-
    -

    If there is no error in the try statements, then nothing is printed. -Either way the function continues on (unless you put a return or -sys.exit() in the except clause). -

    -
    - -

    Restrictions: -

    -

    This command is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the Making -LAMMPS section for more info. -

    -

    Building LAMMPS with the PYTHON package will link LAMMPS with the -Python library on your system. Settings to enable this are in the -lib/python/Makefile.lammps file. See the lib/python/README file for -information on those settings. -

    -

    If you use Python code which calls back to LAMMPS, via the SELF input -argument explained above, there is an extra step required when -building LAMMPS. LAMMPS must also be built as a shared library and -your Python function must be able to to load the Python module in -python/lammps.py that wraps the LAMMPS library interface. These are -the same steps required to use Python by itself to wrap LAMMPS. -Details on these steps are explained in Section -python. Note that it is important that the -stand-alone LAMMPS executable and the LAMMPS shared library be -consistent (built from the same source code files) in order for this -to work. If the two have been built at different times using -different source files, problems may occur. -

    -

    As described above, you can use the python command to invoke a Python -function which calls back to LAMMPS through its Python-wrapped library -interface. However you cannot do the opposite. I.e. you cannot call -LAMMPS from Python and invoke the python command to "callback" to -Python and execute a Python function. LAMMPS will generate an error -if you try to do that. Note that we think there actually should be a -way to do that, but haven't yet been able to figure out how to do it -successfully. -

    -

    Related commands: -

    -

    shell, variable -

    -

    Default: none -

    - diff --git a/doc/doc2/quit.html b/doc/doc2/quit.html deleted file mode 100644 index 7d0883285f..0000000000 --- a/doc/doc2/quit.html +++ /dev/null @@ -1,51 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    quit command -

    -

    Syntax: -

    -
    quit status 
-
    -

    status = numerical exit status (optional) -

    -

    Examples: -

    -

    quit -if "$n > 10000" then "quit 1":pre -

    -

    Description: -

    -

    This command causes LAMMPS to exit, after shutting down all output -cleanly. -

    -

    It can be used as a debug statement in an input script, to terminate -the script at some intermediate point. -

    -

    It can also be used as an invoked command inside the "then" or "else" -portion of an if command. -

    -

    The optional status argument is an integer which signals the return -status to a program calling LAMMPS. A return status of 0 usually -indicates success. A status != 0 is failure, where the specified -value can be used to distinguish the kind of error, e.g. where in the -input script the quit was invoked. If not specified, a status of 0 is -returned. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    if -

    -

    Default: none -

    - diff --git a/doc/doc2/read_data.html b/doc/doc2/read_data.html deleted file mode 100644 index 321f86d2b9..0000000000 --- a/doc/doc2/read_data.html +++ /dev/null @@ -1,1234 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    read_data command -

    -

    Syntax: -

    -
    read_data file keyword args ... 
-
    -
    • file = name of data file to read in - -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = add or offset or shift or extra/atom/types or extra/bond/types or extra/angle/types or extra/dihedral/types or extra/improper/types or group or fix - -
        add arg = append or Nstart or merge
-    append = add new atoms with IDs appended to current IDs
-    Nstart = add new atoms with IDs starting with Nstart
-    merge = add new atoms with their IDs unchanged
-  offset args = toff boff aoff doff ioff
-    toff = offset to add to atom types
-    boff = offset to add to bond types
-    aoff = offset to add to angle types
-    doff = offset to add to dihedral types
-    ioff = offset to add to improper types
-  shift args = Sx Sy Sz
-    Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
-  extra/atom/types arg = # of extra atom types
-  extra/bond/types arg = # of extra bond types
-  extra/angle/types arg = # of extra angle types
-  extra/dihedral/types arg = # of extra dihedral types
-  extra/improper/types arg = # of extra improper types
-  group args = groupID
-    groupID = add atoms in data file to this group
-  fix args = fix-ID header-string section-string
-    fix-ID = ID of fix to process header lines and sections of data file
-    header-string = header lines containing this string will be passed to fix
-    section-string = section names with this string will be passed to fix 
-
      - -
    -

    Examples: -

    -
    read_data data.lj
-read_data ../run7/data.polymer.gz
-read_data data.protein fix mycmap crossterm CMAP 
-read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
-read_data data.water add merge 1 group solvent 
-
    -

    Description: -

    -

    Read in a data file containing information LAMMPS needs to run a -simulation. The file can be ASCII text or a gzipped text file -(detected by a .gz suffix). This is one of 3 ways to specify initial -atom coordinates; see the read_restart and -create_atoms commands for alternative methods. -Also see the explanation of the -restart command-line -switch which can convert a restart file to -a data file. -

    -

    This command can be used multiple times to add new atoms and their -properties to an existing system by using the add, offset, and -shift keywords. See more details below, which includes the use case -for the extra keywords. -

    -

    The group keyword adds all the atoms in the data file to the -specified group-ID. The group will be created if it does not already -exist. This is useful if you are reading multiple data files and wish -to put sets of atoms into different groups so they can be operated on -later. E.g. a group of added atoms can be moved to new positions via -the displace_atoms command. Note that atoms -read from the data file are also always added to the "all" group. The -group command discusses atom groups, as used in LAMMPS. -

    -

    The use of the fix keyword is discussed below. -

    -
    - -

    Reading multiple data files -

    -

    The read_data command can be used multiple times with the same or -different data files to build up a complex system from components -contained in individual data files. For example one data file could -contain fluid in a confined domain; a second could contain wall atoms, -and the second file could be read a third time to create a wall on the -other side of the fluid. The third set of atoms could be rotated to -an opposing direction using the displace_atoms -command, after the third read_data command is used. -

    -

    The add, offset, shift, extra, and group keywords are -useful in this context. -

    -

    If a simulation box does not yet exist, the add keyword -cannot be used; the read_data command is being used for the first -time. If a simulation box does exist, due to using the -create_box command, or a previous read_data command, -then the add keyword must be used. -

    -

    IMPORTANT NOTE: The simulation box size (xlo to xhi, ylo to yhi, zlo -to zhi) in the new data file will be merged with the existing -simulation box to create a large enough box in each dimension to -contain both the existing and new atoms. Each box dimension never -shrinks due to this merge operation, it only stays the same or -grows. Care must be used if you are growing the existing simulation -box in a periodic dimension. If there are existing atoms with bonds -that straddle that periodic boundary, then the atoms may become far -apart if the box size grows. This will separate the atoms in the -bond, which can lead to "lost" bond atoms or bad dynamics. -

    -

    The three choices for the add argument affect how the IDs of atoms -in the data file are treated. If append is specified, atoms in the -data file are added to the current system, with their atom IDs reset -so that an atomID = M in the data file becomes atomID = N+M, where N -is the largest atom ID in the current system. This rule is applied to -all occurrences of atom IDs in the data file, e.g. in the Velocity or -Bonds section. If Nstart is specified, then Nstart is a numeric -value is given, e.g. 1000, so that an atomID = M in the data file -becomes atomID = 1000+M. If merge is specified, the data file atoms -are added to the current system without changing their IDs. They are -assumed to merge (without duplication) with the currently defined -atoms. It is up to you to insure there are no multiply defined atom -IDs, as LAMMPS only performs an incomplete check that this is the case -by insuring the resulting max atomID >= the number of atoms. -

    -

    The offset and shift keywords can only be used if the add -keyword is also specified. -

    -

    The offset keyword adds the specified offset values to the atom -types, bond types, angle types, dihedral types, and improper types as -they are read from the data file. E.g. if toff = 2, and the file -uses atom types 1,2,3, then the added atoms will have atom types -3,4,5. These offsets apply to all occurrences of types in the data -file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs -sections. This makes it easy to use atoms and molecules and their -attributes from a data file in different simulations, where you want -their types (atom, bond, angle, etc) to be different depending on what -other types already exist. All five offset values must be specified, -but individual values will be ignored if the data file does not use -that attribute (e.g. no bonds). -

    -

    The shift keyword can be used to specify an (Sx, Sy, Sz) -displacement applied to the coordinates of each atom. Sz must be 0.0 -for a 2d simulation. This is a mechanism for adding structured -collections of atoms at different locations within the simulation box, -to build up a complex geometry. It is up to you to insure atoms do -not end up overlapping unphysically which would lead to bad dynamics. -Note that the displace_atoms command can be used -to move a subset of atoms after they have been read from a data file. -Likewise, the delete_atoms command can be used to -remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are -also added to the simulation box information (xlo, xhi, ylo, yhi, zlo, -zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo + -Sx, xhi_new = xhi + Sx. -

    -

    The extra keywords can only be used the first time the read_data -command is used. They are useful if you intend to add new atom, bond, -angle, etc types later with additional read_data commands. This is -because the maximum number of allowed atom, bond, angle, etc types is -set by LAMMPS when the system is first initialized. If you do not use -the extra keywords, then the number of these types will be limited -to what appears in the first data file you read. For example, if the -first data file is a solid substrate of Si, it will likely specify a -single atom type. If you read a second data file with a different -material (water molecules) that sit on top of the substrate, you will -want to use different atom types for those atoms. You can only do -this if you set the extra/atom/types keyword to a sufficiently large -value when reading the substrate data file. Note that use of the -extra keywords also allows each data file to contain sections like -Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for -the number of types in that data file. If the offset keyword is -used appropriately when each data file is read, the values in those -sections will be stored correctly in the larger data structures -allocated by the use of the extra keywords. E.g. the substrate file -can list mass and pair coefficients for type 1 silicon atoms. The -water file can list mass and pair coeffcients for type 1 and type 2 -hydrogen and oxygen atoms. Use of the extra and offset keywords -will store those mass and pair coefficient values appropriately in -data structures that allow for 3 atom types (Si, H, O). Of course, -you would still need to specify coefficients for H/Si and O/Si -interactions in your input script to have a complete pairwise -interaction model. -

    -

    An alternative to using the extra keywords with the read_data -command, is to use the create_box command to -initialize the simulation box and all the various type limits you need -via its extra keywords. Then use the read_data command one or more -times to populate the system with atoms, bonds, angles, etc, using the -offset keyword if desired to alter types used in the various data -files you read. -

    -
    - -

    Format of a data file -

    -

    The structure of the data file is important, though many settings and -sections are optional or can come in any order. See the examples -directory for sample data files for different problems. -

    -

    A data file has a header and a body. The header appears first. The -first line of the header is always skipped; it typically contains a -description of the file. Then lines are read one at a time. Lines -can have a trailing comment starting with '#' that is ignored. If the -line is blank (only whitespace after comment is deleted), it is -skipped. If the line contains a header keyword, the corresponding -value(s) is read from the line. If it doesn't contain a header -keyword, the line begins the body of the file. -

    -

    The body of the file contains zero or more sections. The first line -of a section has only a keyword. This line can have a trailing -comment starting with '#' that is either ignored or can be used to -check for a style match, as described below. The next line is -skipped. The remaining lines of the section contain values. The -number of lines depends on the section keyword as described below. -Zero or more blank lines can be used between sections. Sections can -appear in any order, with a few exceptions as noted below. -

    -

    The keyword fix can be used one or more times. Each usage specifies -a fix that will be used to process a specific portion of the data -file. Any header line containing header-string and any section with -a name containing section-string will be passed to the specified -fix. See the fix property/atom command for -an example of a fix that operates in this manner. The doc page for -the fix defines the syntax of the header line(s) and section(s) that -it reads from the data file. Note that the header-string can be -specified as NULL, in which case no header lines are passed to the -fix. This means that it can infer the length of its Section from -standard header settings, such as the number of atoms. -

    -

    The formatting of individual lines in the data file (indentation, -spacing between words and numbers) is not important except that header -and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must -be capitalized as shown and can't have extra white space between their -words - e.g. two spaces or a tab between the 2 words in "xlo xhi" or -the 2 words in "Bond Coeffs", is not valid. -

    -
    - -

    Format of the header of a data file -

    -

    These are the recognized header keywords. Header lines can come in -any order. The value(s) are read from the beginning of the line. -Thus the keyword atoms should be in a line like "1000 atoms"; the -keyword ylo yhi should be in a line like "-10.0 10.0 ylo yhi"; the -keyword xy xz yz should be in a line like "0.0 5.0 6.0 xy xz yz". -All these settings have a default value of 0, except the lo/hi box -size defaults are -0.5 and 0.5. A line need only appear if the value -is different than the default. -

    -
    • atoms = # of atoms in system -
    • bonds = # of bonds in system -
    • angles = # of angles in system -
    • dihedrals = # of dihedrals in system -
    • impropers = # of impropers in system -
    • atom types = # of atom types in system -
    • bond types = # of bond types in system -
    • angle types = # of angle types in system -
    • dihedral types = # of dihedral types in system -
    • improper types = # of improper types in system -
    • extra bond per atom = leave space for this many new bonds per atom -
    • extra angle per atom = leave space for this many new angles per atom -
    • extra dihedral per atom = leave space for this many new dihedrals per atom -
    • extra improper per atom = leave space for this many new impropers per atom -
    • extra special per atom = leave space for this many new special bonds per atom -
    • ellipsoids = # of ellipsoids in system -
    • lines = # of line segments in system -
    • triangles = # of triangles in system -
    • bodies = # of bodies in system -
    • xlo xhi = simulation box boundaries in x dimension -
    • ylo yhi = simulation box boundaries in y dimension -
    • zlo zhi = simulation box boundaries in z dimension -
    • xy xz yz = simulation box tilt factors for triclinic system -
    -

    The initial simulation box size is determined by the lo/hi settings. -In any dimension, the system may be periodic or non-periodic; see the -boundary command. When the simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the processors command. The -partitioning can later be changed by the balance or -fix balance commands. -

    -

    If the xy xz yz line does not appear, LAMMPS will set up an -axis-aligned (orthogonal) simulation box. If the line does appear, -LAMMPS creates a non-orthogonal simulation domain shaped as a -parallelepiped with triclinic symmetry. The parallelepiped has its -"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting -from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = -(xz,yz,zhi-zlo). Xy,xz,yz can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. -

    -

    By default, the tilt factors (xy,xz,yz) can not skew the box more than -half the distance of the corresponding parallel box length. For -example, if xlo = 2 and xhi = 12, then the x box length is 10 and the -xy tilt factor must be between -5 and 5. Similarly, both xz and yz -must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not -a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all geometrically equivalent. If you wish to define a box -with tilt factors that exceed these limits, you can use the box -tilt command, with a setting of large; a setting of -small is the default. -

    -

    See Section_howto 12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used -triclinic representations. -

    -

    When a triclinic system is used, the simulation domain should normally -be periodic in the dimension that the tilt is applied to, which is -given by the second dimension of the tilt factor (e.g. y for xy tilt). -This is so that pairs of atoms interacting across that boundary will -have one of them shifted by the tilt factor. Periodicity is set by -the boundary command. For example, if the xy tilt -factor is non-zero, then the y dimension should be periodic. -Similarly, the z dimension should be periodic if xz or yz is non-zero. -LAMMPS does not require this periodicity, but you may lose atoms if -this is not the case. -

    -

    Also note that if your simulation will tilt the box, e.g. via the fix -deform command, the simulation box must be setup to -be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by -using the change box command with its ortho and -triclinic options. -

    -

    For 2d simulations, the zlo zhi values should be set to bound the z -coords for atoms that appear in the file; the default of -0.5 0.5 is -valid if all z coords are 0.0. For 2d triclinic simulations, the xz -and yz tilt factors must be 0.0. -

    -

    If the system is periodic (in a dimension), then atom coordinates can -be outside the bounds (in that dimension); they will be remapped (in a -periodic sense) back inside the box. Note that if the add option is -being used to add atoms to a simulation box that already exists, this -periodic remapping will be performed using simulation box bounds that -are the union of the existing box and the box boundaries in the new -data file. -

    -

    IMPORTANT NOTE: If the system is non-periodic (in a dimension), then -all atoms in the data file must have coordinates (in that dimension) -that are "greater than or equal to" the lo value and "less than or -equal to" the hi value. If the non-periodic dimension is of style -"fixed" (see the boundary command), then the atom -coords must be strictly "less than" the hi value, due to the way -LAMMPS assign atoms to processors. Note that you should not make the -lo/hi values radically smaller/larger than the extent of the atoms. -For example, if your atoms extend from 0 to 50, you should not specify -the box bounds as -10000 and 10000. This is because LAMMPS uses the -specified box size to layout the 3d grid of processors. A huge -(mostly empty) box will be sub-optimal for performance when using -"fixed" boundary conditions (see the boundary -command). When using "shrink-wrap" boundary conditions (see the -boundary command), a huge (mostly empty) box may cause -a parallel simulation to lose atoms when LAMMPS shrink-wraps the box -around the atoms. The read_data command will generate an error -in this case. -

    -

    The "extra bond per atom" setting (angle, dihedral, improper) is only -needed if new bonds (angles, dihedrals, impropers) will be added to -the system when a simulation runs, e.g. by using the fix -bond/create command. This will pre-allocate -space in LAMMPS data structures for storing the new bonds (angles, -dihedrals, impropers). -

    -

    The "extra special per atom" setting is typically only needed if new -bonds/angles/etc will be added to the system, e.g. by using the fix -bond/create command. Or if entire new molecules -will be added to the system, e.g. by using the fix -deposit or fix pour commands, which -will have more special 1-2,1-3,1-4 neighbors than any other molecules -defined in the data file. Using this setting will pre-allocate space -in the LAMMPS data structures for storing these neighbors. See the -special_bonds and molecule doc -pages for more discussion of 1-2,1-3,1-4 neighbors. -

    -

    IMPORTANT NOTE: All of the "extra" settings are only used if they -appear in the first data file read; see the description of the add -keyword above for reading multiple data files. If they appear in -later data files, they are ignored. -

    -

    The "ellipsoids" and "lines" and "triangles" and "bodies" settings are -only used with atom_style ellipsoid or line or tri or -body and specify how many of the atoms are -finite-size ellipsoids or lines or triangles or bodies; the remainder -are point particles. See the discussion of ellipsoidflag and the -Ellipsoids section below. See the discussion of lineflag and the -Lines section below. See the discussion of triangleflag and the -Triangles section below. See the discussion of bodyflag and the -Bodies section below. -

    -

    IMPORTANT NOTE: For atom_style template, the -molecular topology (bonds,angles,etc) is contained in the molecule -templates read-in by the molecule command. This means -you cannot set the bonds, angles, etc header keywords in the data -file, nor can you define Bonds, Angles, etc sections as discussed -below. You can set the bond types, angle types, etc header -keywords, though it is not necessary. If specified, they must match -the maximum values defined in any of the template molecules. -

    -
    - -

    Format of the body of a data file -

    -

    These are the section keywords for the body of the file. -

    -
    • Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies = atom-property sections -
    • Bonds, Angles, Dihedrals, Impropers = molecular topology sections -
    • Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs = force field sections -
    • BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs = class 2 force field sections -
    -

    These keywords will check an appended comment for a match with the -currently defined style: -

    -
    • Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs -
    -

    For example, these lines: -

    -
    Atoms # sphere
-Pair Coeffs # lj/cut 
-
    -

    will check if the currently-defined atom_style is -sphere, and the current pair_style is lj/cut. If -not, LAMMPS will issue a warning to indicate that the data file -section likely does not contain the correct number or type of -parameters expected for the currently-defined style. -

    -

    Each section is listed below in alphabetic order. The format of each -section is described including the number of lines it must contain and -rules (if any) for where it can appear in the data file. -

    -

    Any individual line in the various sections can have a trailing -comment starting with "#" for annotation purposes. E.g. in the -Atoms section: -

    -
    10 1 17 -1.0 10.0 5.0 6.0   # salt ion 
-
    -
    - -

    Angle Coeffs section: -

    -
    • one line per angle type - -
    • line syntax: ID coeffs - -
        ID = angle type (1-N)
-  coeffs = list of coeffs 
-
      -
    • example: - -
        6 70 108.5 0 0 
-
      - -
    -

    The number and meaning of the coefficients are specific to the defined -angle style. See the angle_style and -angle_coeff commands for details. Coefficients can -also be set via the angle_coeff command in the -input script. -

    -
    - -

    AngleAngle Coeffs section: -

    -
    • one line per improper type - -
    • line syntax: ID coeffs - -
        ID = improper type (1-N)
-  coeffs = list of coeffs (see improper_coeff) 
-
      - -
    -
    - -

    AngleAngleTorsion Coeffs section: -

    -
    • one line per dihedral type - -
    • line syntax: ID coeffs - -
        ID = dihedral type (1-N)
-  coeffs = list of coeffs (see dihedral_coeff) 
-
      - -
    -
    - -

    Angles section: -

    -
    • one line per angle - -
    • line syntax: ID type atom1 atom2 atom3 - -
        ID = number of angle (1-Nangles)
-  type = angle type (1-Nangletype)
-  atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle 
-
      -example: -
      -
        2 2 17 29 430 
-
      - -
    -

    The 3 atoms are ordered linearly within the angle. Thus the central -atom (around which the angle is computed) is the atom2 in the list. -E.g. H,O,H for a water molecule. The Angles section must appear -after the Atoms section. All values in this section must be -integers (1, not 1.0). -

    -
    - -

    AngleTorsion Coeffs section: -

    -
    • one line per dihedral type - -
    • line syntax: ID coeffs - -
        ID = dihedral type (1-N)
-  coeffs = list of coeffs (see dihedral_coeff) 
-
      - -
    -
    - -

    Atoms section: -

    -
    • one line per atom -
    • line syntax: depends on atom style -
    -

    An Atoms section must appear in the data file if natoms > 0 in the -header section. The atoms can be listed in any order. These are the -line formats for each atom style in LAMMPS. As -discussed below, each line can optionally have 3 flags (nx,ny,nz) -appended to it, which indicate which image of a periodic simulation -box the atom is in. These may be important to include for some kinds -of analysis. -

    -
    - - - - - - - - - - - - - - - - - - -
    angle atom-ID molecule-ID atom-type x y z
    atomic atom-ID atom-type x y z
    body atom-ID atom-type bodyflag mass x y z
    bond atom-ID molecule-ID atom-type x y z
    charge atom-ID atom-type q x y z
    dipole atom-ID atom-type q x y z mux muy muz
    electron atom-ID atom-type q spin eradius x y z
    ellipsoid atom-ID atom-type ellipsoidflag density x y z
    full atom-ID molecule-ID atom-type q x y z
    line atom-ID molecule-ID atom-type lineflag density x y z
    meso atom-ID atom-type rho e cv x y z
    molecular atom-ID molecule-ID atom-type x y z
    peri atom-ID atom-type volume density x y z
    smd atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z
    sphere atom-ID atom-type diameter density x y z
    template atom-ID molecule-ID template-index template-atom atom-type x y z
    tri atom-ID molecule-ID atom-type triangleflag density x y z
    wavepacket atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
    hybrid atom-ID atom-type x y z sub-style1 sub-style2 ... -
    - -

    The keywords have these meanings: -

    -
    • atom-ID = integer ID of atom -
    • molecule-ID = integer ID of molecule the atom belongs to -
    • atom-type = type of atom (1-Ntype) -
    • q = charge on atom (charge units) -
    • diameter = diameter of spherical atom (distance units) -
    • ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles -
    • lineflag = 1 for line segment particles, 0 for point particles -
    • triangleflag = 1 for triangular particles, 0 for point particles -
    • bodyflag = 1 for body particles, 0 for point particles -
    • template-index = which molecule within the molecule template the atom is part of -
    • template-atom = which atom within a template molecule the atom is -
    • density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) -
    • mass = mass of particle (mass units) -
    • volume = volume of particle (distance^3 units) -
    • x,y,z = coordinates of atom -
    • mux,muy,muz = components of dipole moment of atom (dipole units) -
    • rho = density (need units) for SPH particles -
    • e = energy (need units) for SPH particles -
    • cv = heat capacity (need units) for SPH particles -
    • spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) -
    • eradius = electron radius (or fixed-core radius) -
    • etag = integer ID of electron that each wavepacket belongs to -
    • cs_re,cs_im = real/imaginary parts of wavepacket coefficients -
    • kernel_radius = ??? (distance units) -
    • contact_radius = ??? (distance units) -
    -

    The units for these quantities depend on the unit style; see the -units command for details. -

    -

    For 2d simulations specify z as 0.0, or a value within the zlo zhi -setting in the data file header. -

    -

    The atom-ID is used to identify the atom throughout the simulation and -in dump files. Normally, it is a unique value from 1 to Natoms for -each atom. Unique values larger than Natoms can be used, but they -will cause extra memory to be allocated on each processor, if an atom -map array is used, but not if an atom map hash is used; see the -atom_modify command for details. If an atom map is -not used (e.g. an atomic system with no bonds), and you don't care if -unique atom IDs appear in dump files, then the atom-IDs can all be set -to 0. -

    -

    The molecule ID is a 2nd identifier attached to an atom. Normally, it -is a number from 1 to N, identifying which molecule the atom belongs -to. It can be 0 if it is an unbonded atom or if you don't care to -keep track of molecule assignments. -

    -

    The diameter specifies the size of a finite-size spherical particle. -It can be set to 0.0, which means that atom is a point particle. -

    -

    The ellipsoidflag, lineflag, triangleflag, and bodyflag determine -whether the particle is a finite-size ellipsoid or line or triangle or -body of finite size, or whether the particle is a point particle. -Additional attributes must be defined for each ellipsoid, line, -triangle, or body in the corresponding Ellipsoids, Lines, -Triangles, or Bodies section. -

    -

    The template-index and template-atom are only defined used by -atom_style template. In this case the -molecule command is used to define a molecule template -which contains one or more molecules. If an atom belongs to one of -those molecules, its template-index and template-atom are both set -to positive integers; if not the values are both 0. The -template-index is which molecule (1 to Nmols) the atom belongs to. -The template-atom is which atom (1 to Natoms) within the molecule -the atom is. -

    -

    Some pair styles and fixes and computes that operate on finite-size -particles allow for a mixture of finite-size and point particles. See -the doc pages of individual commands for details. -

    -

    For finite-size particles, the density is used in conjunction with the -particle volume to set the mass of each particle as mass = density * -volume. In this context, volume can be a 3d quantity (for spheres or -ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line -segments). If the volume is 0.0, meaning a point particle, then the -density value is used as the mass. One exception is for the body atom -style, in which case the mass of each particle (body or point -particle) is specified explicitly. This is because the volume of the -body is unknown. -

    -

    For atom_style hybrid, following the 5 initial values (ID,type,x,y,z), -specific values for each sub-style must be listed. The order of the -sub-styles is the same as they were listed in the -atom_style command. The sub-style specific values -are those that are not the 5 standard ones (ID,type,x,y,z). For -example, for the "charge" sub-style, a "q" value would appear. For -the "full" sub-style, a "molecule-ID" and "q" would appear. These are -listed in the same order they appear as listed above. Thus if -

    -
    atom_style hybrid charge sphere 
-
    -

    were used in the input script, each atom line would have these fields: -

    -
    atom-ID atom-type x y z q diameter density 
-
    -

    Note that if a non-standard value is defined by multiple sub-styles, -it must appear mutliple times in the atom line. E.g. the atom line -for atom_style hybrid dipole full would list "q" twice: -

    -
    atom-ID atom-type x y z q mux muy myz molecule-ID q 
-
    -

    Atom lines specify the (x,y,z) coordinates of atoms. These can be -inside or outside the simulation box. When the data file is read, -LAMMPS wraps coordinates outside the box back into the box for -dimensions that are periodic. As discussed above, if an atom is -outside the box in a non-periodic dimension, it will be lost. -

    -

    LAMMPS always stores atom coordinates as values which are inside the -simulation box. It also stores 3 flags which indicate which image of -the simulation box (in each dimension) the atom would be in if its -coordinates were unwrapped across periodic boundaries. An image flag -of 0 means the atom is still inside the box when unwrapped. A value -of 2 means add 2 box lengths to get the unwrapped coordinate. A value -of -1 means subtract 1 box length to get the unwrapped coordinate. -LAMMPS updates these flags as atoms cross periodic boundaries during -the simulation. The dump command can output atom atom -coordinates in wrapped or unwrapped form, as well as the 3 image -flags. -

    -

    In the data file, atom lines (all lines or none of them) can -optionally list 3 trailing integer values (nx,ny,nz), which are used -to initialize the atom's image flags. If nx,ny,nz values are not -listed in the data file, LAMMPS initializes them to 0. Note that the -image flags are immediately updated if an atom's coordinates need to -wrapped back into the simulation box. -

    -

    It is only important to set image flags correctly in a data file if a -simulation model relies on unwrapped coordinates for some calculation; -otherwise they can be left unspecified. Examples of LAMMPS commands -that use unwrapped coordinates internally are as follows: -

    -
    • Atoms in a rigid body (see fix rigid, fix -rigid/small) must have consistent image flags, so that -when the atoms are unwrapped, they are near each other, i.e. as a -single body. - -
    • If the replicate command is used to generate a larger -system, image flags must be consistent for bonded atoms when the bond -crosses a periodic boundary. I.e. the values of the image flags -should be different by 1 (in the appropriate dimension) for the two -atoms in such a bond. - -
    • If you plan to dump image flags and perform post-analysis -that will unwrap atom coordinates, it may be important that a -continued run (restarted from a data file) begins with image flags -that are consistent with the previous run. -
    -

    Atom velocities and other atom quantities not defined above are set to -0.0 when the Atoms section is read. Velocities can be set later by -a Velocities section in the data file or by a -velocity or set command in the input -script. -

    -
    - -

    Bodies section: -

    -
    • one or more lines per body - -
    • first line syntax: atom-ID ninteger ndouble - -
        ninteger = # of integer quantities for this particle
-  ndouble = # of floating-point quantities for this particle 
-
      -
    • 0 or more integer lines: one line for every 10 integer quantities - -
    • 0 or more double lines: one line for every 10 double quantities - -
    • example: - -
        12 3 6
-  2 3 2
-  1.0 2.0 3.0 1.0 2.0 4.0 
-
      -
    • example: - -
        12 0 14
-  1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
-  2.0 4.0 4.0 2.0 
-
      - -
    -

    The Bodies section must appear if atom_style body -is used and any atoms listed in the Atoms section have a bodyflag = -1. The number of bodies should be specified in the header section via -the "bodies" keyword. -

    -

    Each body can have a variable number of integer and/or floating-point -values. The number and meaning of the values is defined by the body -style, as described in the body doc page. The body style -is given as an argument to the atom_style body -command. -

    -

    The ninteger and ndouble values determine how many integer and -floating-point values are specified for this particle. Ninteger and -ndouble can be as large as needed and can be different for every body. -Integer values are then listed on subsequent lines, 10 values per -line. Floating-point values follow on subsequent lines, again 10 per -line. If the number of lines is not evenly divisible by 10, the last -line in that group contains the remaining values, e.g. 4 values out of -14 in the last example above, for floating-point values. If there are -no values of a particular type, no lines appear for that type, -e.g. there are no integer lines in the last example above. -

    -

    The Bodies section must appear after the Atoms section. -

    -
    - -

    Bond Coeffs section: -

    -
    • one line per bond type - -
    • line syntax: ID coeffs - -
        ID = bond type (1-N)
-  coeffs = list of coeffs 
-
      -
    • example: - -
        4 250 1.49 
-
      - -
    -

    The number and meaning of the coefficients are specific to the defined -bond style. See the bond_style and -bond_coeff commands for details. Coefficients can -also be set via the bond_coeff command in the input -script. -

    -
    - -

    BondAngle Coeffs section: -

    -
    • one line per angle type - -
    • line syntax: ID coeffs - -
        ID = angle type (1-N)
-  coeffs = list of coeffs (see class 2 section of angle_coeff) 
-
      - -
    -
    - -

    BondBond Coeffs section: -

    -
    • one line per angle type - -
    • line syntax: ID coeffs - -
        ID = angle type (1-N)
-  coeffs = list of coeffs (see class 2 section of angle_coeff) 
-
      - -
    -
    - -

    BondBond13 Coeffs section: -

    -
    • one line per dihedral type - -
    • line syntax: ID coeffs - -
        ID = dihedral type (1-N)
-  coeffs = list of coeffs (see class 2 section of dihedral_coeff) 
-
      - -
    -
    - -

    Bonds section: -

    -
    • one line per bond - -
    • line syntax: ID type atom1 atom2 - -
        ID = bond number (1-Nbonds)
-  type = bond type (1-Nbondtype)
-  atom1,atom2 = IDs of 1st,2nd atoms in bond 
-
      -
    • example: - -
        12 3 17 29 
-
      - -
    -

    The Bonds section must appear after the Atoms section. All values -in this section must be integers (1, not 1.0). -

    -
    - -

    Dihedral Coeffs section: -

    -
    • one line per dihedral type - -
    • line syntax: ID coeffs - -
        ID = dihedral type (1-N)
-  coeffs = list of coeffs 
-
      -
    • example: - -
        3 0.6 1 0 1 
-
      - -
    -

    The number and meaning of the coefficients are specific to the defined -dihedral style. See the dihedral_style and -dihedral_coeff commands for details. -Coefficients can also be set via the -dihedral_coeff command in the input script. -

    -
    - -

    Dihedrals section: -

    -
    • one line per dihedral - -
    • line syntax: ID type atom1 atom2 atom3 atom4 - -
        ID = number of dihedral (1-Ndihedrals)
-  type = dihedral type (1-Ndihedraltype)
-  atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral 
-
      -
    • example: - -
        12 4 17 29 30 21 
-
      - -
    -

    The 4 atoms are ordered linearly within the dihedral. The Dihedrals -section must appear after the Atoms section. All values in this -section must be integers (1, not 1.0). -

    -
    - -

    Ellipsoids section: -

    -
    • one line per ellipsoid - -
    • line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk - -
        atom-ID = ID of atom which is an ellipsoid
-  shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
-  quatw,quati,quatj,quatk = quaternion components for orientation of atom 
-
      -
    • example: - -
        12 1 2 1 1 0 0 0 
-
      - -
    -

    The Ellipsoids section must appear if atom_style -ellipsoid is used and any atoms are listed in the -Atoms section with an ellipsoidflag = 1. The number of ellipsoids -should be specified in the header section via the "ellipsoids" -keyword. -

    -

    The 3 shape values specify the 3 diameters or aspect ratios of a -finite-size ellipsoidal particle, when it is oriented along the 3 -coordinate axes. They must all be non-zero values. -

    -

    The values quatw, quati, quatj, and quatk set the orientation -of the atom as a quaternion (4-vector). Note that the shape -attributes specify the aspect ratios of an ellipsoidal particle, which -is oriented by default with its x-axis along the simulation box's -x-axis, and similarly for y and z. If this body is rotated (via the -right-hand rule) by an angle theta around a unit vector (a,b,c), then -the quaternion that represents its new orientation is given by -(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These -4 components are quatw, quati, quatj, and quatk as specified above. -LAMMPS normalizes each atom's quaternion in case (a,b,c) is not -specified as a unit vector. -

    -

    The Ellipsoids section must appear after the Atoms section. -

    -
    - -

    EndBondTorsion Coeffs section: -

    -
    • one line per dihedral type - -
    • line syntax: ID coeffs - -
        ID = dihedral type (1-N)
-  coeffs = list of coeffs (see class 2 section of dihedral_coeff) 
-
      - -
    -
    - -

    Improper Coeffs section: -

    -
    • one line per improper type - -
    • line syntax: ID coeffs - -
        ID = improper type (1-N)
-  coeffs = list of coeffs 
-
      -
    • example: - -
        2 20 0.0548311 
-
      - -
    -

    The number and meaning of the coefficients are specific to the defined -improper style. See the improper_style and -improper_coeff commands for details. -Coefficients can also be set via the -improper_coeff command in the input script. -

    -
    - -

    Impropers section: -

    -
    • one line per improper - -
    • line syntax: ID type atom1 atom2 atom3 atom4 - -
        ID = number of improper (1-Nimpropers)
-  type = improper type (1-Nimpropertype)
-  atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper 
-
      -
    • example: - -
        12 3 17 29 13 100 
-
      - -
    -

    The ordering of the 4 atoms determines the definition of the improper -angle used in the formula for each improper -style. See the doc pages for individual styles -for details. -

    -

    The Impropers section must appear after the Atoms section. All -values in this section must be integers (1, not 1.0). -

    -
    - -

    Lines section: -

    -
    • one line per line segment - -
    • line syntax: atom-ID x1 y1 x2 y2 - -
        atom-ID = ID of atom which is a line segment
-  x1,y1 = 1st end point
-  x2,y2 = 2nd end point 
-
      -
    • example: - -
        12 1.0 0.0 2.0 0.0 
-
      - -
    -

    The Lines section must appear if atom_style line -is used and any atoms are listed in the Atoms section with a -lineflag = 1. The number of lines should be specified in the header -section via the "lines" keyword. -

    -

    The 2 end points are the end points of the line segment. The ordering -of the 2 points should be such that using a right-hand rule to cross -the line segment with a unit vector in the +z direction, gives an -"outward" normal vector perpendicular to the line segment. -I.e. normal = (c2-c1) x (0,0,1). This orientation may be important -for defining some interactions. -

    -

    The Lines section must appear after the Atoms section. -

    -
    - -

    Masses section: -

    -
    • one line per atom type - -
    • line syntax: ID mass - -
        ID = atom type (1-N)
-  mass = mass value 
-
      -
    • example: - -
        3 1.01 
-
      - -
    -

    This defines the mass of each atom type. This can also be set via the -mass command in the input script. This section cannot be -used for atom styles that define a mass for individual atoms - -e.g. atom_style sphere. -

    -
    - -

    MiddleBondTorsion Coeffs section: -

    -
    • one line per dihedral type - -
    • line syntax: ID coeffs - -
        ID = dihedral type (1-N)
-  coeffs = list of coeffs (see class 2 section of dihedral_coeff) 
-
      - -
    -
    - -

    Pair Coeffs section: -

    -
    • one line per atom type - -
    • line syntax: ID coeffs - -
        ID = atom type (1-N)
-  coeffs = list of coeffs 
-
      -
    • example: - -
        3 0.022 2.35197 0.022 2.35197 
-
      - -
    -

    The number and meaning of the coefficients are specific to the defined -pair style. See the pair_style and -pair_coeff commands for details. Since pair -coefficients for types I != J are not specified, these will be -generated automatically by the pair style's mixing rule. See the -individual pair_style doc pages and the pair_modify -mix command for details. Pair coefficients can also -be set via the pair_coeff command in the input -script. -

    -
    - -

    PairIJ Coeffs section: -

    -
    • one line per pair of atom types for all I,J with I <= J - -
    • line syntax: ID1 ID2 coeffs - -
        ID1 = atom type I = 1-N
-  ID2 = atom type J = I-N, with I <= J
-  coeffs = list of coeffs 
-
      -
    • examples: - -
        3 3 0.022 2.35197 0.022 2.35197
-  3 5 0.022 2.35197 0.022 2.35197 
-
      - -
    -

    This section must have N*(N+1)/2 lines where N = # of atom types. The -number and meaning of the coefficients are specific to the defined -pair style. See the pair_style and -pair_coeff commands for details. Since pair -coefficients for types I != J are all specified, these values will -turn off the default mixing rule defined by the pair style. See the -individual pair_style doc pages and the pair_modify -mix command for details. Pair coefficients can also -be set via the pair_coeff command in the input -script. -

    -
    - -

    Triangles section: -

    -
    • one line per triangle - -
    • line syntax: atom-ID x1 y1 x2 y2 - -
        atom-ID = ID of atom which is a line segment
-  x1,y1,z1 = 1st corner point
-  x2,y2,z2 = 2nd corner point
-  x3,y3,z3 = 3rd corner point 
-
      -
    • example: - -
        12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 
-
      - -
    -

    The Triangles section must appear if atom_style -tri is used and any atoms are listed in the Atoms -section with a triangleflag = 1. The number of lines should be -specified in the header section via the "triangles" keyword. -

    -

    The 3 corner points are the corner points of the triangle. The -ordering of the 3 points should be such that using a right-hand rule -to go from point1 to point2 to point3 gives an "outward" normal vector -to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This -orientation may be important for defining some interactions. -

    -

    The Triangles section must appear after the Atoms section. -

    -
    - -

    Velocities section: -

    -
    • one line per atom -
    • line syntax: depends on atom style -
    -
    - - - - -
    all styles except those listed atom-ID vx vy vz
    electron atom-ID vx vy vz ervel
    ellipsoid atom-ID vx vy vz lx ly lz
    sphere atom-ID vx vy vz wx wy wz
    hybrid atom-ID vx vy vz sub-style1 sub-style2 ... -
    - -

    where the keywords have these meanings: -

    -

    vx,vy,vz = translational velocity of atom -lx,ly,lz = angular momentum of aspherical atom -wx,wy,wz = angular velocity of spherical atom -ervel = electron radial velocity (0 for fixed-core):ul -

    -

    The velocity lines can appear in any order. This section can only be -used after an Atoms section. This is because the Atoms section -must have assigned a unique atom ID to each atom so that velocities -can be assigned to them. -

    -

    Vx, vy, vz, and ervel are in units of velocity. Lx, ly, -lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, -Wz are in units of angular velocity (radians/time). -

    -

    For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz), -specific values for each sub-style must be listed. The order of the -sub-styles is the same as they were listed in the -atom_style command. The sub-style specific values -are those that are not the 5 standard ones (ID,vx,vy,vz). For -example, for the "sphere" sub-style, "wx", "wy", "wz" values would -appear. These are listed in the same order they appear as listed -above. Thus if -

    -
    atom_style hybrid electron sphere 
-
    -

    were used in the input script, each velocity line would have these -fields: -

    -
    atom-ID vx vy vz ervel wx wy wz 
-
    -

    Translational velocities can also be set by the -velocity command in the input script. -

    -
    - -

    Restrictions: -

    -

    To read gzipped data files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the Making -LAMMPS section of the documentation. -

    -

    Related commands: -

    -

    read_dump, read_restart, -create_atoms, write_data -

    -

    Default: -

    -

    The default for all the extra keywords is 0. -

    - diff --git a/doc/doc2/read_dump.html b/doc/doc2/read_dump.html deleted file mode 100644 index 3f1a8b124c..0000000000 --- a/doc/doc2/read_dump.html +++ /dev/null @@ -1,336 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    read_dump command -

    -

    Syntax: -

    -
    read_dump file Nstep field1 field2 ... keyword values ... 
-
    -
    • file = name of dump file to read - -
    • Nstep = snapshot timestep to read from file - -
    • one or more fields may be appended - -
      field = x or y or z or vx or vy or vz or q or ix or iy or iz
-  x,y,z = atom coordinates
-  vx,vy,vz = velocity components
-  q = charge
-  ix,iy,iz = image flags in each dimension 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = box or replace or purge or trim or add or label or scaled or wrapped or format - -
        box value = yes or no = replace simulation box with dump box
-  replace value = yes or no = overwrite atoms with dump atoms
-  purge value = yes or no = delete all atoms before adding dump atoms
-  trim value = yes or no = trim atoms not in dump snapshot
-  add value = yes or no = add new dump atoms to system
-  label value = field column
-    field = one of the listed fields or id or type
-    column = label on corresponding column in dump file
-  scaled value = yes or no = coords in dump file are scaled/unscaled
-  wrapped value = yes or no = coords in dump file are wrapped/unwrapped
-  format values = format of dump file, must be last keyword if used
-    native = native LAMMPS dump file
-    xyz = XYZ file
-    molfile style path = VMD molfile plugin interface
-      style = dcd or xyz or others supported by molfile plugins
-      path = optional path for location of molfile plugins 
-
      - -
    -

    Examples: -

    -
    read_dump dump.file 5000 x y z
-read_dump dump.xyz 5 x y z box no format xyz
-read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
-read_dump dump.dcd 0 x y z box yes format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
-read_dump dump.file 5000 x y vx vy trim yes
-read_dump ../run7/dump.file.gz 10000 x y z box yes 
-read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
-read_dump dump.dcd 0 x y z format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile 
-
    -

    Description: -

    -

    Read atom information from a dump file to overwrite the current atom -coordinates, and optionally the atom velocities and image flags and -the simluation box dimensions. This is useful for restarting a run -from a particular snapshot in a dump file. See the -read_restart and read_data -commands for alternative methods to do this. Also see the -rerun command for a means of reading multiple snapshots -from a dump file. -

    -

    Note that a simulation box must already be defined before using the -read_dump command. This can be done by the -create_box, read_data, or -read_restart commands. The read_dump command can -reset the simulation box dimensions, as explained below. -

    -

    Also note that reading per-atom information from a dump snapshot is -limited to the atom coordinates, velocities and image flags, as -explained below. Other atom properties, which may be necessary to run -a valid simulation, such as atom charge, or bond topology information -for a molecular system, are not read from (or even contained in) dump -files. Thus this auxiliary information should be defined in the usual -way, e.g. in a data file read in by a read_data -command, before using the read_dump command, or by the set -command, after the dump snapshot is read. -

    -
    - -

    If the dump filename specified as file ends with ".gz", the dump -file is read in gzipped format. You cannot (yet) read a dump file -that was written in binary format with a ".bin" suffix, or to multiple -files via the "%" option in the dump file name. See the -dump command for details. -

    -

    The format of the dump file is selected through the format keyword. -If specified, it must be the last keyword used, since all remaining -arguments are passed on to the dump reader. The native format is -for native LAMMPS dump files, written with a dump atom or -dump custom command. The xyz format is for generic XYZ -formatted dump files. These formats take no additional values. -

    -

    The molfile format supports reading data through using the VMD -molfile plugin interface. This dump reader format is only available, -if the USER-MOLFILE package has been installed when compiling -LAMMPS. -

    -

    The molfile format takes one or two additional values. The style -value determines the file format to be used and can be any format that -the molfile plugins support, such as DCD or XYZ. Note that DCD dump -files can be written by LAMMPS via the dump dcd command. -The path value specifies a list of directories which LAMMPS will -search for the molfile plugins appropriate to the specified style. -The syntax of the path value is like other search paths: it can -contain multiple directories separated by a colon (or semi-colon on -windows). The path keyword is optional and defaults to ".", -i.e. the current directory. -

    -

    Support for other dump format readers may be added in the future. -

    -
    - -

    Global information is first read from the dump file, namely timestep -and box information. -

    -

    The dump file is scanned for a snapshot with a time stamp that matches -the specified Nstep. This means the LAMMPS timestep the dump file -snapshot was written on for the native format. Note that the xyz -and molfile formats do not store the timestep. For these formats, -timesteps are numbered logically, in a sequential manner, starting -from 0. Thus to access the 10th snapshot in an xyz or mofile -formatted dump file, use Nstep = 9. -

    -

    The dimensions of the simulation box for the selected snapshot are -also read; see the box keyword discussion below. For the native -format, an error is generated if the snapshot is for a triclinic box -and the current simulation box is orthogonal or vice versa. A warning -will be generated if the snapshot box boundary conditions (periodic, -shrink-wrapped, etc) do not match the current simulation boundary -conditions, but the boundary condition information in the snapshot is -otherwise ignored. See the "boundary" command for more details. -

    -

    For the xyz format, no information about the box is available, so -you must set the box flag to no. See details below. -

    -

    For the molfile format, reading simulation box information is -typically supported, but the location of the simulation box origin is -lost and no explicit information about periodicity or -orthogonal/triclinic box shape is available. The USER-MOLFILE package -makes a best effort to guess based on heuristics, but this may not -always work perfectly. -

    -
    - -

    Per-atom information from the dump file snapshot is then read from the -dump file snapshot. This corresponds to the specified fields listed -in the read_dump command. It is an error to specify a z-dimension -field, namely z, vz, or iz, for a 2d simulation. -

    -

    For dump files in native format, each column of per-atom data has a -text label listed in the file. A matching label for each field must -appear, e.g. the label "vy" for the field vy. For the x, y, z -fields any of the following labels are considered a match: -

    -
    x, xs, xu, xsu for field x
-y, ys, yu, ysu for field y
-z, zs, zu, zsu for field z 
-
    -

    The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and -unwrapped) is explained on the dump command doc page. -These labels are searched for in the list of column labels in the dump -file, in order, until a match is found. -

    -

    The dump file must also contain atom IDs, with a column label of "id". -

    -

    If the add keyword is specified with a value of yes, as discussed -below, the dump file must contain atom types, with a column label of -"type". -

    -

    If a column label you want to read from the dump file is not a match -to a specified field, the label keyword can be used to specify the -specific column label from the dump file to associate with that field. -An example is if a time-averaged coordinate is written to the dump -file via the fix ave/atom command. The column -will then have a label corresponding to the fix-ID rather than "x" or -"xs". The label keyword can also be used to specify new column -labels for fields id and type. -

    -

    For dump files in xyz format, only the x, y, and z fields are -supported. The dump file does not store atom IDs, so these are -assigned consecutively to the atoms as they appear in the dump file, -starting from 1. Thus you should insure that order of atoms is -consistent from snapshot to snapshot in the the XYZ dump file. See -the dump_modify sort command if the XYZ dump file -was written by LAMMPS. -

    -

    For dump files in molfile format, the x, y, z, vx, vy, and -vz fields can be specified. However, not all molfile formats store -velocities, or their respective plugins may not support reading of -velocities. The molfile dump files do not store atom IDs, so these -are assigned consecutively to the atoms as they appear in the dump -file, starting from 1. Thus you should insure that order of atoms are -consistent from snapshot to snapshot in the the molfile dump file. -See the dump_modify sort command if the dump file -was written by LAMMPS. -

    -
    - -

    Information from the dump file snapshot is used to overwrite or -replace properties of the current system. There are various options -for how this is done, determined by the specified fields and optional -keywords. -

    -

    The timestep of the snapshot becomes the current timestep for the -simulation. See the reset_timestep command if -you wish to change this after the dump snapshot is read. -

    -

    If the box keyword is specified with a yes value, then the current -simulation box dimensions are replaced by the dump snapshot box -dimensions. If the box keyword is specified with a no value, the -current simulatoin box is unchanged. -

    -

    If the purge keyword is specified with a yes value, then all -current atoms in the system are deleted before any of the operations -invoked by the replace, trim, or add keywords take place. -

    -

    If the replace keyword is specified with a yes value, then atoms -with IDs that are in both the current system and the dump snapshot -have their properties overwritten by field values. If the replace -keyword is specified with a no value, atoms with IDs that are in -both the current system and the dump snapshot are not modified. -

    -

    If the trim keyword is specified with a yes value, then atoms with -IDs that are in the current system but not in the dump snapshot are -deleted. These atoms are unaffected if the trim keyword is -specified with a no value. -

    -

    If the add keyword is specified with a yes value, then atoms with -IDs that are in the dump snapshot, but not in the current system are -added to the system. These dump atoms are ignored if the add -keyword is specified with a no value. -

    -

    Note that atoms added via the add keyword will have only the -attributes read from the dump file due to the field arguments. If -x or y or z is not specified as a field, a value of 0.0 is used -for added atoms. Added atoms must have an atom type, so this value -must appear in the dump file. -

    -

    Any other attributes (e.g. charge or particle diameter for spherical -particles) will be set to default values, the same as if the -create_atoms command were used. -

    -

    Note that atom IDs are not preserved for new dump snapshot atoms added -via the add keyword. The procedure for assigning new atom IDS to -added atoms is the same as is described for the -create_atoms command. -

    -
    - -

    Atom coordinates read from the dump file are first converted into -unscaled coordinates, relative to the box dimensions of the snapshot. -These coordinates are then be assigned to an existing or new atom in -the current simulation. The coordinates will then be remapped to the -simulation box, whether it is the original box or the dump snapshot -box. If periodic boundary conditions apply, this means the atom will -be remapped back into the simulation box if necessary. If shrink-wrap -boundary conditions apply, the new coordinates may change the -simulation box dimensions. If fixed boundary conditions apply, the -atom will be lost if it is outside the simulation box. -

    -

    For native format dump files, the 3 xyz image flags for an atom in -the dump file are set to the corresponding values appearing in the -dump file if the ix, iy, iz fields are specified. If not -specified, the image flags for replaced atoms are not changed and -image flags for new atoms are set to default values. If coordinates -read from the dump file are in unwrapped format (e.g. xu) then the -image flags for read-in atoms are also set to default values. The -remapping procedure described in the previous paragraph will then -change images flags for all atoms (old and new) if periodic boundary -conditions are applied to remap an atom back into the simulation box. -

    -

    IMPORTANT NOTE: If you get a warning about inconsistent image flags -after reading in a dump snapshot, it means one or more pairs of bonded -atoms now have inconsistent image flags. As discussed in Section -errors this may or may not cause problems for -subsequent simulations, One way this can happen is if you read image -flag fields from the dump file but do not also use the dump file box -parameters. -

    -

    LAMMPS knows how to compute unscaled and remapped coordinates for the -snapshot column labels discussed above, e.g. x, xs, xu, xsu. -If another column label is assigned to the x or y or z field via -the label keyword, e.g. for coordinates output by the fix -ave/atom command, then LAMMPS needs to know whether -the coordinate information in the dump file is scaled and/or wrapped. -This can be set via the scaled and wrapped keywords. Note that -the value of the scaled and wrapped keywords is ignored for fields -x or y or z if the label keyword is not used to assign a -column label to that field. -

    -

    The scaled/unscaled and wrapped/unwrapped setting must be identical -for any of the x, y, z fields that are specified. Thus you -cannot read xs and yu from the dump file. Also, if the dump file -coordinates are scaled and the simulation box is triclinic, then all 3 -of the x, y, z fields must be specified, since they are all -needed to generate absolute, unscaled coordinates. -

    -
    - -

    Restrictions: -

    -

    To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the Making -LAMMPS section of the documentation. -

    -

    The molfile dump file formats are part of the USER-MOLFILE package. -They are only enabled if LAMMPS was built with that packages. See the -Making LAMMPS section for more info. -

    -

    Related commands: -

    -

    dump, dump molfile, -read_data, read_restart, -rerun -

    -

    Default: -

    -

    The option defaults are box = yes, replace = yes, purge = no, trim = -no, add = no, scaled = no, wrapped = yes, and format = native. -

    - diff --git a/doc/doc2/read_restart.html b/doc/doc2/read_restart.html deleted file mode 100644 index 66afe6a1b6..0000000000 --- a/doc/doc2/read_restart.html +++ /dev/null @@ -1,223 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    read_restart command -

    -

    Syntax: -

    -
    read_restart file flag 
-
    -
    • file = name of binary restart file to read in -
    • flag = remap (optional) -
    -

    Examples: -

    -
    read_restart save.10000
-read_restart save.10000 remap
-read_restart restart.*
-read_restart restart.*.mpiio
-read_restart poly.*.% remap 
-
    -
    -
    -

    Description: -

    -

    Read in a previously saved system configuration from a restart file. -This allows continuation of a previous run. Details about what -information is stored (and not stored) in a restart file is given -below. Basically this operation will re-create the simulation box -with all its atoms and their attributes as well as some related global -settings, at the point in time it was written to the restart file by a -previous simluation. The simulation box will be partitioned into a -regular 3d grid of rectangular bricks, one per processor, based on the -number of processors in the current simulation and the settings of the -processors command. The partitioning can later be -changed by the balance or fix -balance commands. -

    -

    IMPORTANT NOTE: Normally, restart files are written by the -restart or write_restart commands -so that all atoms in the restart file are inside the simulation box. -If this is not the case, the read_restart command will print an error -that atoms were "lost" when the file is read. This error should be -reported to the LAMMPS developers so the invalid writing of the -restart file can be fixed. If you still wish to use the restart file, -the optional remap flag can be appended to the read_restart command. -This should avoid the error, by explicitly remapping each atom back into -the simulation box, updating image flags for the atom appropriately. -

    -

    Restart files are saved in binary format to enable exact restarts, -meaning that the trajectories of a restarted run will precisely match -those produced by the original run had it continued on. -

    -

    Several things can prevent exact restarts due to round-off effects, in -which case the trajectories in the 2 runs will slowly diverge. These -include running on a different number of processors or changing -certain settings such as those set by the newton or -processors commands. LAMMPS will issue a warning in -these cases. -

    -

    Certain fixes will not restart exactly, though they should provide -statistically similar results. These include fix -shake and fix langevin. -

    -

    Certain pair styles will not restart exactly, though they should -provide statistically similar results. This is because the forces -they compute depend on atom velocities, which are used at half-step -values every timestep when forces are computed. When a run restarts, -forces are initially evaluated with a full-step velocity, which is -different than if the run had continued. These pair styles include -granular pair styles, pair dpd, and -pair lubricate. -

    -

    If a restarted run is immediately different than the run which -produced the restart file, it could be a LAMMPS bug, so consider -reporting it if you think the behavior is -wrong. -

    -

    Because restart files are binary, they may not be portable to other -machines. In this case, you can use the -restart command-line -switch to convert a restart file to a data -file. -

    -

    Similar to how restart files are written (see the -write_restart and restart -commands), the restart filename can contain two wild-card characters. -If a "*" appears in the filename, the directory is searched for all -filenames that match the pattern where "*" is replaced with a timestep -value. The file with the largest timestep value is read in. Thus, -this effectively means, read the latest restart file. It's useful if -you want your script to continue a run from where it left off. See -the run command and its "upto" option for how to specify -the run command so it doesn't need to be changed either. -

    -

    If a "%" character appears in the restart filename, LAMMPS expects a -set of multiple files to exist. The restart and -write_restart commands explain how such sets are -created. Read_restart will first read a filename where "%" is -replaced by "base". This file tells LAMMPS how many processors -created the set and how many files are in it. Read_restart then reads -the additional files. For example, if the restart file was specified -as save.% when it was written, then read_restart reads the files -save.base, save.0, save.1, ... save.P-1, where P is the number of -processors that created the restart file. -

    -

    Note that P could be the total number of processors in the previous -simulation, or some subset of those processors, if the fileper or -nfile options were used when the restart file was written; see the -restart and write_restart commands -for details. The processors in the current LAMMPS simulation share -the work of reading these files; each reads a roughly equal subset of -the files. The number of processors which created the set can be -different the number of processors in the current LAMMPS simulation. -This can be a fast mode of input on parallel machines that support -parallel I/O. -

    -

    A restart file can also be read in parallel as one large binary file -via the MPI-IO library, assuming it was also written with MPI-IO. -MPI-IO is part of the MPI standard for versions 2.0 and above. Using -MPI-IO requires two steps. First, build LAMMPS with its MPIIO package -installed, e.g. -

    -
    make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform 
-
    -

    Second, use a restart filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO dump files, a particular restart file must be both -written and read using MPI-IO. -

    -
    - -

    A restart file stores the following information about a simulation: -units, atom style and atom style related settings (id, map, -sort), communication settings (mode, cutoff, vel), timestep, -simulation box size and shape and boundary settings, group -definitions, per-type atom settings such as mass, per-atom attributes -including their group assignments and molecular topology attributes, -force field styles and - in most cases - force field coefficients, and -special_bonds settings. This means that commands -for these quantities do not need to be re-specified in the input -script that reads the restart file, though you can redefine settings -after the restart file is read. -

    -

    One exception is that some force styles (pair, bond, angle, etc) do -not store their coefficient info in restart files. Typically these -are many-body or tabulated potentials which read their parameters from -separate files; you may need to re-specify the pair -style and pair coeff commands in -your restart input script. The doc pages for individual pair styles -mention if this is the case. This is also true of bond_style hybrid -(and angle_style, dihedral_style, improper_style hybrid). -

    -

    All settings made by the pair_modify command, such -as the shift and tail settings, are stored in the restart file with -the pair style. The one exception is the pair_modify -compute setting is not stored, since it is typically -only used for debugging purposes. -

    -

    Information about kspace_style settings are not -stored in the restart file. Hence if you wish to use an Ewald or PPPM -solver, these commands must be re-issued after the restart file is -read. -

    -

    The list of fixes used for a simulation is not stored in -the restart file. This means the new input script should specify all -fixes it will use. Note that some fixes store an internal "state" -which is written to the restart file. This allows the fix to continue -on with its calculations in a restarted simulation. To re-enable such -a fix, the fix command in the new input script must use the same -fix-ID and group-ID as was used in the input script that wrote the -restart file. If a match is found, LAMMPS prints a message indicating -that the fix is being re-enabled. If no match is found before the -first run or minimization is performed by the new script, the "state" -information for the saved fix is discarded. See the doc pages for -individual fixes for info on which ones can be restarted in this -manner. -

    -

    Bond interactions (angle, etc) that have been turned off by the fix -shake or delete_bonds command will -be written to a restart file as if they are turned on. This means -they will need to be turned off again in a new run after the restart -file is read. -

    -

    Bonds that are broken (e.g. by a bond-breaking potential) are written -to the restart file as broken bonds with a type of 0. Thus these -bonds will still be broken when the restart file is read. -

    -

    Bonds that have been broken by the fix -bond/break command have disappeared from the -system. No information about these bonds is written to the restart -file. -

    -

    IMPORTANT NOTE: No other information is stored in the restart file. -This means that an input script that reads a restart file should -specify settings for quantities like timestep size, -thermodynamic, neighbor list -criteria including settings made via the -neigh_modify comand, dump file -output, geometric regions, etc. -

    -
    - -

    Restrictions: -

    -

    To write and read restart files in parallel with MPI-IO, the MPIIO -package must be installed. -

    -

    Related commands: -

    -

    read_data, read_dump, -write_restart, restart -

    -

    Default: none -

    - diff --git a/doc/doc2/region.html b/doc/doc2/region.html deleted file mode 100644 index a1a454856c..0000000000 --- a/doc/doc2/region.html +++ /dev/null @@ -1,327 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    region command -

    -

    Syntax: -

    -
    region ID style args keyword arg ... 
-
    -
    • ID = user-assigned name for the region - -
    • style = delete or block or cone or cylinder or plane or prism or sphere or union or intersect - -
        delete = no args
-  block args = xlo xhi ylo yhi zlo zhi
-    xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
-  cone args = dim c1 c2 radlo radhi lo hi
-    dim = x or y or z = axis of cone
-    c1,c2 = coords of cone axis in other 2 dimensions (distance units)
-    radlo,radhi = cone radii at lo and hi end (distance units)
-    lo,hi = bounds of cone in dim (distance units)
-  cylinder args = dim c1 c2 radius lo hi
-    dim = x or y or z = axis of cylinder
-    c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
-    radius = cylinder radius (distance units)
-      radius can be a variable (see below)
-    lo,hi = bounds of cylinder in dim (distance units)
-  plane args = px py pz nx ny nz
-    px,py,pz = point on the plane (distance units)
-    nx,ny,nz = direction normal to plane (distance units)
-  prism args = xlo xhi ylo yhi zlo zhi xy xz yz
-    xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
-    xy = distance to tilt y in x direction (distance units)
-    xz = distance to tilt z in x direction (distance units)
-    yz = distance to tilt z in y direction (distance units)
-  sphere args = x y z radius
-    x,y,z = center of sphere (distance units)
-    radius = radius of sphere (distance units)
-      radius can be a variable (see below)
-  union args = N reg-ID1 reg-ID2 ...
-    N = # of regions to follow, must be 2 or greater
-    reg-ID1,reg-ID2, ... = IDs of regions to join together
-  intersect args = N reg-ID1 reg-ID2 ...
-    N = # of regions to follow, must be 2 or greater
-    reg-ID1,reg-ID2, ... = IDs of regions to intersect 
-
      -
    • zero or more keyword/arg pairs may be appended - -
    • keyword = side or units or move or rotate - -
        side value = in or out
-    in = the region is inside the specified geometry
-    out = the region is outside the specified geometry
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units
-  move args = v_x v_y v_z
-    v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
-  rotate args = v_theta Px Py Pz Rx Ry Rz
-    v_theta = equal-style variable for rotaton of region over time (in radians)
-    Px,Py,Pz = origin for axis of rotation (distance units)
-    Rx,Ry,Rz = axis of rotation vector 
-
      - -
    -

    Examples: -

    -
    region 1 block -3.0 5.0 INF 10.0 INF INF
-region 2 sphere 0.0 0.0 0.0 5 side out
-region void cylinder y 2 3 5 -5.0 EDGE units box
-region 1 prism 0 10 0 10 0 10 2 0 0
-region outside union 4 side1 side2 side3 side4
-region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL 
-
    -

    Description: -

    -

    This command defines a geometric region of space. Various other -commands use regions. For example, the region can be filled with -atoms via the create_atoms command. Or a bounding -box around the region, can be used to define the simulation box via -the create_box command. Or the atoms in the region -can be identified as a group via the group command, or -deleted via the delete_atoms command. Or the -surface of the region can be used as a boundary wall via the fix -wall/region command. -

    -

    Commands which use regions typically test whether an atom's position -is contained in the region or not. For this purpose, coordinates -exactly on the region boundary are considered to be interior to the -region. This means, for example, for a spherical region, an atom on -the sphere surface would be part of the region if the sphere were -defined with the side in keyword, but would not be part of the -region if it were defined using the side out keyword. See more -details on the side keyword below. -

    -

    Normally, regions in LAMMPS are "static", meaning their geometric -extent does not change with time. If the move or rotate keyword -is used, as described below, the region becomes "dynamic", meaning -it's location or orientation changes with time. This may be useful, -for example, when thermostatting a region, via the compute temp/region -command, or when the fix wall/region command uses a region surface as -a bounding wall on particle motion, i.e. a rotating container. -

    -

    The delete style removes the named region. Since there is little -overhead to defining extra regions, there is normally no need to do -this, unless you are defining and discarding large numbers of regions -in your input script. -

    -

    The lo/hi values for block or cone or cylinder or prism styles -can be specified as EDGE or INF. EDGE means they extend all the way -to the global simulation box boundary. Note that this is the current -box boundary; if the box changes size during a simulation, the region -does not. INF means a large negative or positive number (1.0e20), so -it should encompass the simulation box even if it changes size. If a -region is defined before the simulation box has been created (via -create_box or read_data or -read_restart commands), then an EDGE or INF -parameter cannot be used. For a prism region, a non-zero tilt -factor in any pair of dimensions cannot be used if both the lo/hi -values in either of those dimensions are INF. E.g. if the xy tilt is -non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi. -

    -

    IMPORTANT NOTE: Regions in LAMMPS do not get wrapped across periodic -boundaries, as specified by the boundary command. For -example, a spherical region that is defined so that it overlaps a -periodic boundary is not treated as 2 half-spheres, one on either side -of the simulation box. -

    -

    IMPORTANT NOTE: Regions in LAMMPS are always 3d geometric objects, -regardless of whether the dimension of a simulation -is 2d or 3d. Thus when using regions in a 2d simulation, you should -be careful to define the region so that its intersection with the 2d -x-y plane of the simulation has the 2d geometric extent you want. -

    -

    For style cone, an axis-aligned cone is defined which is like a -cylinder except that two different radii (one at each end) can be -defined. Either of the radii (but not both) can be 0.0. -

    -

    For style cone and cylinder, the c1,c2 params are coordinates in -the 2 other dimensions besides the cylinder axis dimension. For dim = -x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. -Thus the third example above specifies a cylinder with its axis in the -y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and -extending in the y-direction from -5.0 to the upper box boundary. -

    -

    For style plane, a plane is defined which contain the point -(px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does -not have to be of unit length. The "inside" of the plane is the -half-space in the direction of the normal vector; see the discussion -of the side option below. -

    -

    For style prism, a parallelepiped is defined (it's too hard to spell -parallelepiped in an input script!). The parallelepiped has its -"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting -from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = -(xz,yz,zhi-zlo). Xy,xz,yz can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. -

    -

    A prism region that will be used with the create_box -command to define a triclinic simulation box must have tilt factors -(xy,xz,yz) that do not skew the box more than half the distance of -corresponding the parallel box length. For example, if xlo = 2 and -xhi = 12, then the x box length is 10 and the xy tilt factor must be -between -5 and 5. Similarly, both xz and yz must be between --(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, -since if the maximum tilt factor is 5 (as in this example), then -configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all -geometrically equivalent. -

    -

    The radius value for style sphere and cylinder can be specified -as an equal-style variable. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the radius of the region. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent radius. -

    -

    See Section_howto 12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used -triclinic representations. -

    -

    The union style creates a region consisting of the volume of all the -listed regions combined. The intersect style creates a region -consisting of the volume that is common to all the listed regions. -

    -

    IMPORTANT NOTE: The union and intersect regions operate by -invoking methods from their list of sub-regions. Thus you cannot -delete the sub-regions after defining the union or intersection -region. -

    -
    - -

    The side keyword determines whether the region is considered to be -inside or outside of the specified geometry. Using this keyword in -conjunction with union and intersect regions, complex geometries -can be built up. For example, if the interior of two spheres were -each defined as regions, and a union style with side = out was -constructed listing the region-IDs of the 2 spheres, the resulting -region would be all the volume in the simulation box that was outside -both of the spheres. -

    -

    The units keyword determines the meaning of the distance units used -to define the region for any argument above listed as having distance -units. It also affects the scaling of the velocity vector specfied -with the vel keyword, the amplitude vector specified with the -wiggle keyword, and the rotation point specified with the rotate -keyword, since they each involve a distance metric. -

    -

    A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. -A lattice value means the distance units are in lattice spacings. -The lattice command must have been previously used to -define the lattice spacings which are used as follows: -

    -
    • For style block, the lattice spacing in dimension x is applied to -xlo and xhi, similarly the spacings in dimensions y,z are applied to -ylo/yhi and zlo/zhi. - -
    • For style cone, the lattice spacing in argument dim is applied to -lo and hi. The spacings in the two radial dimensions are applied to -c1 and c2. The two cone radii are scaled by the lattice -spacing in the dimension corresponding to c1. - -
    • For style cylinder, the lattice spacing in argument dim is applied -to lo and hi. The spacings in the two radial dimensions are applied -to c1 and c2. The cylinder radius is scaled by the lattice -spacing in the dimension corresponding to c1. - -
    • For style plane, the lattice spacing in dimension x is applied to -px and nx, similarly the spacings in dimensions y,z are applied to -py/ny and pz/nz. - -
    • For style prism, the lattice spacing in dimension x is applied to -xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing -in dimension x is applied to xy and xz, and the spacing in dimension y -to yz. - -
    • For style sphere, the lattice spacing in dimensions x,y,z are -applied to the sphere center x,y,z. The spacing in dimension x is -applied to the sphere radius. -
    -
    - -

    If the move or rotate keywords are used, the region is "dynamic", -meaning its location or orientation changes with time. These keywords -cannot be used with a union or intersect style region. Instead, -the keywords should be used to make the individual sub-regions of the -union or intersect region dynamic. Normally, each sub-region -should be "dynamic" in the same manner (e.g. rotate around the same -point), though this is not a requirement. -

    -

    The move keyword allows one or more equal-style -variables to be used to specify the x,y,z displacement -of the region, typically as a function of time. A variable is -specified as v_name, where name is the variable name. Any of the -three variables can be specified as NULL, in which case no -displacement is calculated in that dimension. -

    -

    Note that equal-style variables can specify formulas with various -mathematical functions, and include thermo_style -command keywords for the simulation box parameters and timestep and -elapsed time. Thus it is easy to specify a region displacement that -change as a function of time or spans consecutive runs in a continuous -fashion. For the latter, see the start and stop keywords of the -run command and the elaplong keyword of thermo_style -custom for details. -

    -

    For example, these commands would displace a region from its initial -position, in the positive x direction, effectively at a constant -velocity: -

    -
    variable dx equal ramp(0,10)
-region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL 
-
    -

    Note that the initial displacemet is 0.0, though that is not required. -

    -

    Either of these varaibles would "wiggle" the region back and forth in -the y direction: -

    -
    variable dy equal swiggle(0,5,100)
-variable dysame equal 5*sin(2*PI*elaplong*dt/100)
-region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL 
-
    -

    The rotate keyword rotates the region around a rotation axis R = -(Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz). The rotation -angle is calculated, presumably as a function of time, by a variable -specified as v_theta, where theta is the variable name. The variable -should generate its result in radians. The direction of rotation for -the region around the rotation axis is consistent with the right-hand -rule: if your right-hand thumb points along R, then your fingers -wrap around the axis in the direction of rotation. -

    -

    The move and rotate keywords can be used together. In this case, -the displacement specified by the move keyword is applied to the P -point of the rotate keyword. -

    -

    Restrictions: -

    -

    A prism cannot be of 0.0 thickness in any dimension; use a small z -thickness for 2d simulations. For 2d simulations, the xz and yz -parameters must be 0.0. -

    -

    Related commands: -

    -

    lattice, create_atoms, -delete_atoms, group -

    -

    Default: -

    -

    The option defaults are side = in, units = lattice, and no move or -rotation. -

    - diff --git a/doc/doc2/replicate.html b/doc/doc2/replicate.html deleted file mode 100644 index 6b1bac3821..0000000000 --- a/doc/doc2/replicate.html +++ /dev/null @@ -1,100 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    replicate command -

    -

    Syntax: -

    -
    replicate nx ny nz 
-
    -
    • nx,ny,nz = replication factors in each dimension -
    -

    Examples: -

    -
    replicate 2 3 2 
-
    -

    Description: -

    -

    Replicate the current simulation one or more times in each dimension. -For example, replication factors of 2,2,2 will create a simulation -with 8x as many atoms by doubling the simulation domain in each -dimension. A replication factor of 1 in a dimension leaves the -simulation domain unchanged. When the new simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the processors command. The -partitioning can later be changed by the balance or -fix balance commands. -

    -

    All properties of the atoms are replicated, including their -velocities, which may or may not be desirable. New atom IDs are -assigned to new atoms, as are molecule IDs. Bonds and other topology -interactions are created between pairs of new atoms as well as between -old and new atoms. This is done by using the image flag for each atom -to "unwrap" it out of the periodic box before replicating it. -

    -

    This means that any molecular bond you specify in the original data -file that crosses a periodic boundary should be between two atoms with -image flags that differ by 1. This will allow the bond to be -unwrapped appropriately. -

    -

    Restrictions: -

    -

    A 2d simulation cannot be replicated in the z dimension. -

    -

    If a simulation is non-periodic in a dimension, care should be used -when replicating it in that dimension, as it may put atoms nearly on -top of each other. -

    -

    IMPORTANT NOTE: You cannot use the replicate command on a system which -has a molecule that spans the box and is bonded to itself across a -periodic boundary, so that the molecule is efffectively a loop. A -simple example would be a linear polymer chain that spans the -simulation box and bonds back to itself across the periodic boundary. -More realistic examples would be a CNT (meant to be an infinitely long -CNT) or a graphene sheet or a bulk periodic crystal where there are -explicit bonds specified between near neighbors. (Note that this only -applies to systems that have permanent bonds as specified in the data -file. A CNT that is just atoms modeled with the AIREBO -potential has no such permanent bonds, so it can be -replicated.) The reason replication does not work with those systems -is that the image flag settings described above cannot be made -consistent. I.e. it is not possible to define images flags so that -when every pair of bonded atoms is unwrapped (using the image flags), -they will be close to each other. The only way the replicate command -could work in this scenario is for it to break a bond, insert more -atoms, and re-connect the loop for the larger simulation box. But it -is not clever enough to do this. So you will have to construct a -larger version of your molecule as a pre-processing step and input a -new data file to LAMMPS. -

    -

    If the current simulation was read in from a restart file (before a -run is performed), there can have been no fix information stored in -the file for individual atoms. Similarly, no fixes can be defined at -the time the replicate command is used that require vectors of atom -information to be stored. This is because the replicate command does -not know how to replicate that information for new atoms it creates. -

    -

    Replicating a system that has rigid bodies (defined via the fix -rigid command), either currently defined or that -created the restart file which was read in before replicating, can -cause problems if there is a bond between a pair of rigid bodies that -straddle a periodic boundary. This is because the periodic image -information for particles in the rigid bodies are set differently than -for a non-rigid system and can result in a new bond being created that -spans the periodic box. Thus you cannot use the replicate command in -this scenario. -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/rerun.html b/doc/doc2/rerun.html deleted file mode 100644 index 8bb6b2951d..0000000000 --- a/doc/doc2/rerun.html +++ /dev/null @@ -1,210 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    rerun command -

    -

    Syntax: -

    -
    rerun file1 file2 ... keyword args ... 
-
    -
    • file1,file2,... = dump file(s) to read - -
    • one or more keywords may be appended, keyword dump must appear and be last - -
      keyword = first or last or every or skip or start or stop or dump
- first args = Nfirts
-   Nfirst = dump timestep to start on
- last args = Nlast
-   Nlast = dumptimestep to stop on
- every args = Nevery
-   Nevery = read snapshots matching every this many timesteps
- skip args = Nskip
-   Nskip = read one out of every Nskip snapshots
- start args = Nstart
-   Nstart = timestep on which pseudo run will start
- stop args = Nstop
-   Nstop = timestep to which pseudo run will end
- dump args = same as read_dump command starting with its field arguments 
-
      - -
    -

    Examples: -

    -
    rerun dump.file dump x y z vx vy vz
-rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z
-rerun dump.vels dump x y z vx vy vz box yes format molfile lammpstrj
-rerun dump.dcd dump x y z box no format molfile dcd
-rerun ../run7/dump.file.gz skip 2 dump x y z box yes 
-
    -

    Description: -

    -

    Perform a psuedo simulation run where atom information is read one -snapshot at a time from a dump file(s), and energies and forces are -computed on the shapshot to produce thermodynamic or other output. -

    -

    This can be useful in the following kinds of scenarios, after an -initial simulation produced the dump file: -

    -
    • Compute the energy and forces of snaphots using a different potential. - - -
    • Calculate one or more diagnostic quantities on the snapshots that -weren't computed in the initial run. These can also be computed with -settings not used in the initial run, e.g. computing an RDF via the -compute rdf command with a longer cutoff than was -used initially. - -
    • Calculate the portion of per-atom forces resulting from a subset of -the potential. E.g. compute only Coulombic forces. This can be done -by only defining only a Coulombic pair style in the rerun script. -Doing this in the original script would result in different (bad) -dynamics. -
    -

    Conceptually, using the rerun command is like running an input script -that has a loop in it (see the next and jump -commands). Each iteration of the loop reads one snapshot from the -dump file via the read_dump command, sets the -timestep to the appropriate value, and then invokes a run -command for zero timesteps to simply compute energy and forces, and -any other thermodynamic output or diagnostic info -you have defined. This computation also invokes any fixes you have -defined that apply constraints to the system, such as fix -shake or fix indent. -

    -

    Note that a simulation box must already be defined before using the -rerun command. This can be done by the create_box, -read_data, or read_restart -commands. -

    -

    Also note that reading per-atom information from dump snapshots is -limited to the atom coordinates, velocities and image flags as -explained in the read_dump command. Other atom -properties, which may be necessary to compute energies and forces, -such as atom charge, or bond topology information for a molecular -system, are not read from (or even contained in) dump files. Thus -this auxiliary information should be defined in the usual way, e.g. in -a data file read in by a read_data command, before -using the rerun command. -

    -
    - -

    If more than one dump file is specified, the dump files are read one -after the other. It is assumed that snapshot timesteps will be in -ascending order. If a snapshot is encountered that is not in -ascending order, it will cause the rerun command to complete. -

    -

    The first, last, every, skip keywords determine which -snapshots are read from the dump file(s). Snapshots are skipped until -they have a timestamp >= Nfirst. When a snapshot with a timestamp > -Nlast is encountered, the rerun command finishes. Note below that -the defaults for first and last are to read all snapshots. If the -every keyword is set to a value > 0, then only snapshots with -timestamps that are a multiple of Nevery are read (the first -snapshot is always read). If Nevery = 0, then this criterion is -ignored, i.e. every snapshot is read that meets the other criteria. -If the skip keyword is used, then after the first snapshot is read, -every Nth snapshot is read, where N = Nskip. E.g. if Nskip = 3, -then only 1 out of every 3 snapshots is read, assuming the snapshot -timestamp is also consistent with the other criteria. -

    -

    The start and stop keywords do not affect which snapshots are read -from the dump file(s). Rather, they have the same meaning that they -do for the run command. They only need to be defined if -(a) you are using a fix command that changes some value -over time, and (b) you want the reference point for elapsed time (from -start to stop) to be different than the first and last settings. -See the doc page for individual fixes to see which ones can be used -with the start/stop keywords. Note that if you define neither of -the start/stop or first/last keywords, then LAMMPS treats the -pseudo run as going from 0 to a huge value (effectively infinity). -This means that any quantity that a fix scales as a fraction of -elapsed time in the run, will essentially remain at its intiial value. -Also note that an error will occur if you read a snapshot from the -dump file with a timestep value larger than the stop setting you -have specified. -

    -

    The dump keyword is required and must be the last keyword specified. -Its arguments are passed internally to the read_dump -command. The first argument following the dump keyword should be -the field1 argument of the read_dump command. See -the read_dump doc page for details on the various -options it allows for extracting information from the dump file -snapshots, and for using that information to alter the LAMMPS -simulation. -

    -
    - -

    In general, a LAMMPS input script that uses a rerun command can -include and perform all the usual operations of an input script that -uses the run command. There are a few exceptions and -points to consider, as discussed here. -

    -

    Fixes that perform time integration, such as fix nve or -fix npt are not invoked, since no time integration is -performed. Fixes that perturb or constrain the forces on atoms will -be invoked, just as they would during a normal run. Examples are fix -indent and fix langevin. So you -should think carefully as to whether that makes sense for the manner -in which you are reprocessing the dump snapshots. -

    -

    If you only want the rerun script to perform analyses that do not -involve pair interactions, such as use compute msd to calculated -displacements over time, you do not need to define a pair -style, which may also mean neighbor lists will not -need to be calculated which saves time. The comm_modify -cutoff command can also be used to insure ghost -atoms are acquired from far enough away for operations like bond and -angle evaluations, if no pair style is being used. -

    -

    Every time a snapshot is read, the timestep for the simulation is -reset, as if the reset_timestep command were -used. This command has some restrictions as to what fixes can be -defined. See its doc page for details. For example, the fix -deposit and fix dt/reset fixes -are in this category. They also make no sense to use with a rerun -command. -

    -

    If time-averaging fixes like fix ave/time are -used, they are invoked on timesteps that are a function of their -Nevery, Nrepeat, and Nfreq settings. As an example, see the -fix ave/time doc page for details. You must -insure those settings are consistent with the snapshot timestamps that -are read from the dump file(s). If an averaging fix is not invoked on -a timestep it expects to be, LAMMPS will flag an error. -

    -

    The various forms of LAMMPS output, as defined by the -thermo_style, thermo, -dump, and restart commands occur on -specific timesteps. If successvive dump snapshots skip those -timesteps, then no output will be produced. E.g. if you request -thermodynamic output every 100 steps, but the dump file snapshots are -every 1000 steps, then you will only see thermodynamic output every -1000 steps. -

    -
    - -

    Restrictions: -

    -

    To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the Making -LAMMPS section of the documentation. -

    -

    Related commands: -

    -

    read_dump -

    -

    Default: -

    -

    The option defaults are first = 0, last = a huge value (effectively -infinity), start = same as first, stop = same as last, every = 0, skip -= 1; -

    - diff --git a/doc/doc2/reset_timestep.html b/doc/doc2/reset_timestep.html deleted file mode 100644 index 5e678cb592..0000000000 --- a/doc/doc2/reset_timestep.html +++ /dev/null @@ -1,66 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    reset_timestep command -

    -

    Syntax: -

    -
    reset_timestep N 
-
    -
    • N = timestep number -
    -

    Examples: -

    -
    reset_timestep 0
-reset_timestep 4000000 
-
    -

    Description: -

    -

    Set the timestep counter to the specified value. This command -normally comes after the timestep has been set by reading a restart -file via the read_restart command, or a previous -simulation advanced the timestep. -

    -

    The read_data and create_box -commands set the timestep to 0; the read_restart -command sets the timestep to the value it had when the restart file -was written. -

    -

    Restrictions: none -

    -

    This command cannot be used when any fixes are defined that keep track -of elapsed time to perform certain kinds of time-dependent operations. -Examples are the fix deposit and fix -dt/reset commands. The former adds atoms on -specific timesteps. The latter keeps track of accumulated time. -

    -

    Various fixes use the current timestep to calculate related -quantities. If the timestep is reset, this may produce unexpected -behavior, but LAMMPS allows the fixes to be defined even if the -timestep is reset. For example, commands which thermostat the system, -e.g. fix nvt, allow you to specify a target temperature -which ramps from Tstart to Tstop which may persist over several runs. -If you change the timestep, you may induce an instantaneous change in -the target temperature. -

    -

    Resetting the timestep clears flags for computes that -may have calculated some quantity from a previous run. This means -these quantity cannot be accessed by a variable in between runs until -a new run is performed. See the variable command for -more details. -

    -

    Related commands: -

    -

    rerun -

    -

    Default: none -

    - diff --git a/doc/doc2/restart.html b/doc/doc2/restart.html deleted file mode 100644 index 083e74e024..0000000000 --- a/doc/doc2/restart.html +++ /dev/null @@ -1,187 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    restart command -

    -

    Syntax: -

    -
    restart 0
-restart N root keyword value ...
-restart N file1 file2 keyword value ... 
-
    -
    • N = write a restart file every this many timesteps - -
    • N can be a variable (see below) - -
    • root = filename to which timestep # is appended - -
    • file1,file2 = two full filenames, toggle between them when writing file - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = fileper or nfile - -
        fileper arg = Np
-    Np = write one file for every this many processors
-  nfile arg = Nf
-    Nf = write this many files, one from each of Nf processors 
-
      - -
    -

    Examples: -

    -
    restart 0
-restart 1000 poly.restart
-restart 1000 poly.restart.mpiio
-restart 1000 restart.*.equil
-restart 10000 poly.%.1 poly.%.2 nfile 10
-restart v_mystep poly.restart 
-
    -

    Description: -

    -

    Write out a binary restart file with the current state of the -simulation every so many timesteps, in either or both of two modes, as -a run proceeds. A value of 0 means do not write out any restart -files. The two modes are as follows. If one filename is specified, a -series of filenames will be created which include the timestep in the -filename. If two filenames are specified, only 2 restart files will -be created, with those names. LAMMPS will toggle between the 2 names -as it writes successive restart files. -

    -

    Note that you can specify the restart command twice, once with a -single filename and once with two filenames. This would allow you, -for example, to write out archival restart files every 100000 steps -using a single filenname, and more frequent temporary restart files -every 1000 steps, using two filenames. Using restart 0 will turn off -both modes of output. -

    -

    Similar to dump files, the restart filename(s) can contain -two wild-card characters. -

    -

    If a "*" appears in the single filename, it is replaced with the -current timestep value. This is only recognized when a single -filename is used (not when toggling back and forth). Thus, the 3rd -example above creates restart files as follows: restart.1000.equil, -restart.2000.equil, etc. If a single filename is used with no "*", -then the timestep value is appended. E.g. the 2nd example above -creates restart files as follows: poly.restart.1000, -poly.restart.2000, etc. -

    -

    If a "%" character appears in the restart filename(s), then one file -is written for each processor and the "%" character is replaced with -the processor ID from 0 to P-1. An additional file with the "%" -replaced by "base" is also written, which contains global information. -For example, the files written on step 1000 for filename restart.% -would be restart.base.1000, restart.0.1000, restart.1.1000, ..., -restart.P-1.1000. This creates smaller files and can be a fast mode -of output and subsequent input on parallel machines that support -parallel I/O. The optional fileper and nfile keywords discussed -below can alter the number of files written. -

    -

    The restart file can also be written in parallel as one large binary -file via the MPI-IO library, which is part of the MPI standard for -versions 2.0 and above. Using MPI-IO requires two steps. First, -build LAMMPS with its MPIIO package installed, e.g. -

    -
    make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform 
-
    -

    Second, use a restart filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO dump files, a particular restart file must be both -written and read using MPI-IO. -

    -

    Restart files are written on timesteps that are a multiple of N but -not on the first timestep of a run or minimization. You can use the -write_restart command to write a restart file -before a run begins. A restart file is not written on the last -timestep of a run unless it is a multiple of N. A restart file is -written on the last timestep of a minimization if N > 0 and the -minimization converges. -

    -

    Instead of a numeric value, N can be specifed as an equal-style -variable, which should be specified as v_name, where -name is the variable name. In this case, the variable is evaluated at -the beginning of a run to determine the next timestep at which a -restart file will be written out. On that timestep, the variable will -be evaluated again to determine the next timestep, etc. Thus the -variable should return timestep values. See the stagger() and -logfreq() and stride() math functions for equal-style -variables, as examples of useful functions to use in -this context. Other similar math functions could easily be added as -options for equal-style variables. -

    -

    For example, the following commands will write restart files -every step from 1100 to 1200, and could be useful for debugging -a simulation where something goes wrong at step 1163: -

    -
    variable	s equal stride(1100,1200,1)
-restart		v_s tmp.restart 
-
    -
    - -

    See the read_restart command for information about -what is stored in a restart file. -

    -

    Restart files can be read by a read_restart -command to restart a simulation from a particular state. Because the -file is binary (to enable exact restarts), it may not be readable on -another machine. In this case, you can use the -r command-line -switch to convert a restart file to a data -file. -

    -

    IMPORTANT NOTE: Although the purpose of restart files is to enable -restarting a simulation from where it left off, not all information -about a simulation is stored in the file. For example, the list of -fixes that were specified during the initial run is not stored, which -means the new input script must specify any fixes you want to use. -Even when restart information is stored in the file, as it is for some -fixes, commands may need to be re-specified in the new input script, -in order to re-use that information. See the -read_restart command for information about what is -stored in a restart file. -

    -
    - -

    The optional nfile or fileper keywords can be used in conjunction -with the "%" wildcard character in the specified restart file name(s). -As explained above, the "%" character causes the restart file to be -written in pieces, one piece for each of P processors. By default P = -the number of processors the simulation is running on. The nfile or -fileper keyword can be used to set P to a smaller value, which can -be more efficient when running on a large number of processors. -

    -

    The nfile keyword sets P to the specified Nf value. For example, if -Nf = 4, and the simulation is running on 100 processors, 4 files will -be written, by processors 0,25,50,75. Each will collect information -from itself and the next 24 processors and write it to a restart file. -

    -

    For the fileper keyword, the specified value of Np means write one -file for every Np processors. For example, if Np = 4, every 4th -processor (0,4,8,12,etc) will collect information from itself and the -next 3 processors and write it to a restart file. -

    -
    - -

    Restrictions: -

    -

    To write and read restart files in parallel with MPI-IO, the MPIIO -package must be installed. -

    -

    Related commands: -

    -

    write_restart, read_restart -

    -

    Default: -

    -
    restart 0 
-
    - diff --git a/doc/doc2/run.html b/doc/doc2/run.html deleted file mode 100644 index 3ccb7bb700..0000000000 --- a/doc/doc2/run.html +++ /dev/null @@ -1,215 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    run command -

    -

    Syntax: -

    -
    run N keyword values ... 
-
    -
    • N = # of timesteps - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = upto or start or stop or pre or post or every - -
        upto value = none
-  start value = N1
-    N1 = timestep at which 1st run started
-  stop value = N2
-    N2 = timestep at which last run will end
-  pre value = no or yes
-  post value = no or yes 
-  every values = M c1 c2 ...
-    M = break the run into M-timestep segments and invoke one or more commands between each segment
-    c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
-    c1 = NULL means no command will be invoked 
-
      - -
    -

    Examples: -

    -
    run 10000
-run 1000000 upto
-run 100 start 0 stop 1000
-run 1000 pre no post yes
-run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'"
-run 100000 every 1000 NULL 
-
    -

    Description: -

    -

    Run or continue dynamics for a specified number of timesteps. -

    -

    When the run style is respa, N refers to outer -loop (largest) timesteps. -

    -

    A value of N = 0 is acceptable; only the thermodynamics of the system -are computed and printed without taking a timestep. -

    -

    The upto keyword means to perform a run starting at the current -timestep up to the specified timestep. E.g. if the current timestep -is 10,000 and "run 100000 upto" is used, then an additional 90,000 -timesteps will be run. This can be useful for very long runs on a -machine that allocates chunks of time and terminate your job when time -is exceeded. If you need to restart your script multiple times -(reading in the last restart file), you can keep restarting your -script with the same run command until the simulation finally -completes. -

    -

    The start or stop keywords can be used if multiple runs are being -performed and you want a fix command that changes some -value over time (e.g. temperature) to make the change across the -entire set of runs and not just a single run. See the doc page for -individual fixes to see which ones can be used with the start/stop -keywords. -

    -

    For example, consider this fix followed by 10 run commands: -

    -
    fix	     1 all nvt 200.0 300.0 1.0
-run	     1000 start 0 stop 10000
-run	     1000 start 0 stop 10000
-...
-run	     1000 start 0 stop 10000 
-
    -

    The NVT fix ramps the target temperature from 200.0 to 300.0 during a -run. If the run commands did not have the start/stop keywords (just -"run 1000"), then the temperature would ramp from 200.0 to 300.0 -during the 1000 steps of each run. With the start/stop keywords, the -ramping takes place over the 10000 steps of all runs together. -

    -

    The pre and post keywords can be used to streamline the setup, -clean-up, and associated output to the screen that happens before and -after a run. This can be useful if you wish to do many short runs in -succession (e.g. LAMMPS is being called as a library which is doing -other computations between successive short LAMMPS runs). -

    -

    By default (pre and post = yes), LAMMPS creates neighbor lists, -computes forces, and imposes fix constraints before every run. And -after every run it gathers and prints timings statistics. If a run is -just a continuation of a previous run (i.e. no settings are changed), -the initial computation is not necessary; the old neighbor list is -still valid as are the forces. So if pre is specified as "no" then -the initial setup is skipped, except for printing thermodynamic info. -Note that if pre is set to "no" for the very 1st run LAMMPS -performs, then it is overridden, since the initial setup computations -must be done. -

    -

    IMPORTANT NOTE: If your input script changes the system between 2 -runs, then the initial setup must be performed to insure the change is -recognized by all parts of the code that are affected. Examples are -adding a fix or dump or compute, -changing a neighbor list parameter, or writing -restart file which can migrate atoms between processors. LAMMPS has -no easy way to check if this has happened, but it is an error to use -the pre no option in this case. -

    -

    If post is specified as "no", the full timing summary is skipped; -only a one-line summary timing is printed. -

    -

    The every keyword provides a means of breaking a LAMMPS run into a -series of shorter runs. Optionally, one or more LAMMPS commands (c1, -c2, ..., cN) will be executed in between the short runs. If used, the -every keyword must be the last keyword, since it has a variable -number of arguments. Each of the trailing arguments is a single -LAMMPS command, and each command should be enclosed in quotes, so that -the entire command will be treated as a single argument. This will -also prevent any variables in the command from being evaluated until -it is executed multiple times during the run. Note that if a command -itself needs one of its arguments quoted (e.g. the print -command), then you can use a combination of single and double quotes, -as in the example above or below. -

    -

    The every keyword is a means to avoid listing a long series of runs -and interleaving commands in your input script. For example, a -print command could be invoked or a fix could -be redefined, e.g. to reset a thermostat temperature. Or this could -be useful for invoking a command you have added to LAMMPS that wraps -some other code (e.g. as a library) to perform a computation -periodically during a long LAMMPS run. See this -section of the documentation for info about how -to add new commands to LAMMPS. See this -section of the documentation for ideas -about how to couple LAMMPS to other codes. -

    -

    With the every option, N total steps are simulated, in shorter runs -of M steps each. After each M-length run, the specified commands are -invoked. If only a single command is specified as NULL, then no -command is invoked. Thus these lines: -

    -
    variable q equal x[100]
-run 6000 every 2000 "print 'Coord = $q'" 
-
    -

    are the equivalent of: -

    -
    variable q equal x[100]
-run 2000
-print "Coord = $q"
-run 2000
-print "Coord = $q"
-run 2000
-print "Coord = $q" 
-
    -

    which does 3 runs of 2000 steps and prints the x-coordinate of a -particular atom between runs. Note that the variable "$q" will -be evaluated afresh each time the print command is executed. -

    -

    Note that by using the line continuation character "&", the run every -command can be spread across many lines, though it is still a single -command: -

    -
    run 100000 every 1000 &
-  "print 'Minimum value = $a'" &
-  "print 'Maximum value = $b'" &
-  "print 'Temp = $c'" &
-  "print 'Press = $d'" 
-
    -

    If the pre and post options are set to "no" when used with the -every keyword, then the 1st run will do the full setup and the last -run will print the full timing summary, but these operations will be -skipped for intermediate runs. -

    -

    IMPORTANT NOTE: You might hope to specify a command that exits the run -by jumping out of the loop, e.g. -

    -
    variable t equal temp
-run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" 
-
    -

    Unfortunately this will not currently work. The run command simply -executes each command one at a time each time it pauses, then -continues the run. You can replace the jump command with a simple -quit command and cause LAMMPS to exit during the -middle of a run when the condition is met. -

    -

    Restrictions: -

    -

    When not using the upto keyword, the number of specified timesteps N -must fit in a signed 32-bit integer, so you are limited to slightly -more than 2 billion steps (2^31) in a single run. When using upto, -N can be larger than a signed 32-bit integer, however the difference -between N and the current timestep must still be no larger than -2^31 steps. -

    -

    However, with or without the upto keyword, you can perform -successive runs to run a simulation for any number of steps (ok, up to -2^63 total steps). I.e. the timestep counter within LAMMPS is a -64-bit signed integer. -

    -

    Related commands: -

    -

    minimize, run_style, -temper -

    -

    Default: -

    -

    The option defaults are start = the current timestep, stop = current -timestep + N, pre = yes, and post = yes. -

    - diff --git a/doc/doc2/run_style.html b/doc/doc2/run_style.html deleted file mode 100644 index 2e12bbac8c..0000000000 --- a/doc/doc2/run_style.html +++ /dev/null @@ -1,298 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    run_style command -

    -

    Syntax: -

    -
    run_style style args 
-
    -
    • style = verlet or verlet/split or respa or respa/omp - -
        verlet args = none
-  verlet/split args = none
-  respa args = N n1 n2 ... keyword values ...
-    N = # of levels of rRESPA
-    n1, n2, ... = loop factor between rRESPA levels (N-1 values)
-    zero or more keyword/value pairings may be appended to the loop factors
-    keyword = bond or angle or dihedral or improper or
-	      pair or inner or middle or outer or hybrid or kspace
-      bond value = M
-        M = which level (1-N) to compute bond forces in
-      angle value = M
-        M = which level (1-N) to compute angle forces in
-      dihedral value = M
-        M = which level (1-N) to compute dihedral forces in
-      improper value = M
-        M = which level (1-N) to compute improper forces in
-      pair value = M
-        M = which level (1-N) to compute pair forces in
-      inner values = M cut1 cut2
-        M = which level (1-N) to compute pair inner forces in
-	cut1 = inner cutoff between pair inner and
-	       pair middle or outer  (distance units)
-	cut2 = outer cutoff between pair inner and
-	       pair middle or outer  (distance units)
-      middle values = M cut1 cut2
-        M = which level (1-N) to compute pair middle forces in
-	cut1 = inner cutoff between pair middle and pair outer (distance units)
-	cut2 = outer cutoff between pair middle and pair outer (distance units)
-      outer value = M
-        M = which level (1-N) to compute pair outer forces in
-      hybrid values = M1 [M2 ...] (as many values as there are hybrid sub-styles 
-        M1 = which level (1-N) to compute the first pair_style hybrid sub-style in
-        M2 = which level (1-N) to compute the second pair_style hybrid sub-style in
-        ...
-      kspace value = M
-        M = which level (1-N) to compute kspace forces in 
-
      - -
    -

    Examples: -

    -
    run_style verlet
-run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
-run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 
-
    -
    run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 
-
    -

    Description: -

    -

    Choose the style of time integrator used for molecular dynamics -simulations performed by LAMMPS. -

    -

    The verlet style is a standard velocity-Verlet integrator. -

    -
    - -

    The verlet/split style is also a velocity-Verlet integrator, but it -splits the force calculation within each timestep over 2 partitions of -processors. See Section_start 6 for an -explanation of the -partition command-line switch. -

    -

    Specifically, this style performs all computation except the -kspace_style portion of the force field on the 1st -partition. This include the pair style, bond -style, neighbor list building, -fixes including time intergration, and output. The -kspace_style portion of the calculation is -performed on the 2nd partition. -

    -

    This is most useful for the PPPM kspace_style when its performance on -a large number of processors degrades due to the cost of communication -in its 3d FFTs. In this scenario, splitting your P total processors -into 2 subsets of processors, P1 in the 1st partition and P2 in the -2nd partition, can enable your simulation to run faster. This is -because the long-range forces in PPPM can be calculated at the same -time as pair-wise and bonded forces are being calculated, and the FFTs -can actually speed up when running on fewer processors. -

    -

    To use this style, you must define 2 partitions where P1 is a multiple -of P2. Typically having P1 be 3x larger than P2 is a good choice. -The 3d processor layouts in each partition must overlay in the -following sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by -Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly -for Py1 a multiple of Py2, and Pz1 a multiple of Pz2. -

    -

    Typically the best way to do this is to let the 1st partition choose -its onn optimal layout, then require the 2nd partition's layout to -match the integer multiple constraint. See the -processors command with its part keyword for a way -to control this, e.g. -

    -
    procssors * * * part 1 2 multiple 
-
    -

    You can also use the partition command to explicitly -specity the processor layout on each partition. E.g. for 2 partitions -of 60 and 15 processors each: -

    -
    partition yes 1 processors 3 4 5
-partition yes 2 processors 3 1 5 
-
    -

    When you run in 2-partition mode with the verlet/split style, the -thermodyanmic data for the entire simulation will be output to the log -and screen file of the 1st partition, which are log.lammps.0 and -screen.0 by default; see the "-plog and -pscreen command-line -switches"Section_start.html#start_7 to change this. The log and -screen file for the 2nd partition will not contain thermodynamic -output beyone the 1st timestep of the run. -

    -

    See Section_accelerate of the manual for -performance details of the speed-up offered by the verlet/split -style. One important performance consideration is the assignemnt of -logical processors in the 2 partitions to the physical cores of a -parallel machine. The processors command has -options to support this, and strategies are discussed in -Section_accelerate of the manual. -

    -
    - -

    The respa style implements the rRESPA multi-timescale integrator -(Tuckerman) with N hierarchical levels, where level 1 is -the innermost loop (shortest timestep) and level N is the outermost -loop (largest timestep). The loop factor arguments specify what the -looping factor is between levels. N1 specifies the number of -iterations of level 1 for a single iteration of level 2, N2 is the -iterations of level 2 per iteration of level 3, etc. N-1 looping -parameters must be specified. -

    -

    The timestep command sets the timestep for the -outermost rRESPA level. Thus if the example command above for a -4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep -would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that -specify number of timesteps (e.g. neigh_modify -parameters, dump every N timesteps, etc) refer to the -outermost timesteps. -

    -

    The rRESPA keywords enable you to specify at what level of the -hierarchy various forces will be computed. If not specified, the -defaults are that bond forces are computed at level 1 (innermost -loop), angle forces are computed where bond forces are, dihedral -forces are computed where angle forces are, improper forces are -computed where dihedral forces are, pair forces are computed at the -outermost level, and kspace forces are computed where pair forces are. -The inner, middle, outer forces have no defaults. -

    -

    The inner and middle keywords take additional arguments for -cutoffs that are used by the pairwise force computations. If the 2 -cutoffs for inner are 5.0 and 6.0, this means that all pairs up to -6.0 apart are computed by the inner force. Those between 5.0 and 6.0 -have their force go ramped to 0.0 so the overlap with the next regime -(middle or outer) is smooth. The next regime (middle or outer) will -compute forces for all pairs from 5.0 outward, with those from 5.0 to -6.0 having their value ramped in an inverse manner. -

    -

    Only some pair potentials support the use of the inner and middle -and outer keywords. If not, only the pair keyword can be used -with that pair style, meaning all pairwise forces are computed at the -same rRESPA level. See the doc pages for individual pair styles for -details.i -

    -

    Another variant to use pair potentials in rRESPA is with the hybrid -keyword, which requires the use of a hybrid pair_style -In this scenario, different sub-styles of the hybrid pair style are -evaluated at different rRESPA levels. Thus the hybrid keyword requires -as many level assignments as there are hybrid substyles which designate -the respective sub-styles to the rRESPA level according to their order -of definition in the pair_style command. Since the hybrid designates -pair force computations, it is mututally exclusive with either the pair -or the inner/middle/outer keywords. -

    -

    When using rRESPA (or for any MD simulation) care must be taken to -choose a timestep size(s) that insures the Hamiltonian for the chosen -ensemble is conserved. For the constant NVE ensemble, total energy -must be conserved. Unfortunately, it is difficult to know a priori -how well energy will be conserved, and a fairly long test simulation -(~10 ps) is usually necessary in order to verify that no long-term -drift in energy occurs with the trial set of parameters. -

    -

    With that caveat, a few rules-of-thumb may be useful in selecting -respa settings. The following applies mostly to biomolecular -simulations using the CHARMM or a similar all-atom force field, but -the concepts are adaptable to other problems. Without SHAKE, bonds -involving hydrogen atoms exhibit high-frequency vibrations and require -a timestep on the order of 0.5 fmsec in order to conserve energy. The -relatively inexpensive force computations for the bonds, angles, -impropers, and dihedrals can be computed on this innermost 0.5 fmsec -step. The outermost timestep cannot be greater than 4.0 fmsec without -risking energy drift. Smooth switching of forces between the levels -of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2 -angstrom "healing distance" (the distance between the outer and inner -cutoffs) works reasonably well. We thus recommend the following -settings for use of the respa style without SHAKE in biomolecular -simulations: -

    -
    timestep  4.0
-run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4 
-
    -

    With these settings, users can expect good energy conservation and -roughly a 2.5 fold speedup over the verlet style with a 0.5 fmsec -timestep. -

    -

    If SHAKE is used with the respa style, time reversibility is lost, -but substantially longer time steps can be achieved. For biomolecular -simulations using the CHARMM or similar all-atom force field, bonds -involving hydrogen atoms exhibit high frequency vibrations and require -a time step on the order of 0.5 fmsec in order to conserve energy. -These high frequency modes also limit the outer time step sizes since -the modes are coupled. It is therefore desirable to use SHAKE with -respa in order to freeze out these high frequency motions and increase -the size of the time steps in the respa hierarchy. The following -settings can be used for biomolecular simulations with SHAKE and -rRESPA: -

    -
    fix             2 all shake 0.000001 500 0 m 1.0 a 1
-timestep        4.0
-run_style	respa 2 2 inner 1 4.0 5.0 outer 2 
-
    -

    With these settings, users can expect good energy conservation and -roughly a 1.5 fold speedup over the verlet style with SHAKE and a -2.0 fmsec timestep. -

    -

    For non-biomolecular simulations, the respa style can be -advantageous if there is a clear separation of time scales - fast and -slow modes in the simulation. Even a LJ system can benefit from -rRESPA if the interactions are divided by the inner, middle and outer -keywords. A 2-fold or more speedup can be obtained while maintaining -good energy conservation. In real units, for a pure LJ fluid at -liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1 -Kcal/mol, the following settings seem to work well: -

    -
    timestep  36.0  
-run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 
-
    -
    - -

    The respa/omp styles is a variant of respa adapted for use with -pair, bond, angle, dihedral, improper, or kspace styles with an omp -suffix. It is functionally equivalent to respa but performs additional -operations required for managing omp styles. For more on omp styles -see the Section_accelerate of the manual. -Accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. -

    -

    You can specify respa/omp explicitly in your input script, or -you can use the -suffix command-line switch -when you invoke LAMMPS, or you can use the suffix -command in your input script. -

    -

    See Section_accelerate of the manual for -more instructions on how to use the accelerated styles effectively. -

    -
    - -

    Restrictions: -

    -

    The verlet/split style can only be used if LAMMPS was built with the -REPLICA package. Correspondingly the respa/omp style is available only -if the USER-OMP package was included. See the Making LAMMPS -section for more info on packages. -

    -

    Whenever using rRESPA, the user should experiment with trade-offs in -speed and accuracy for their system, and verify that they are -conserving energy to adequate precision. -

    -

    Related commands: -

    -

    timestep, run -

    -

    Default: -

    -
    run_style verlet 
-
    -
    - - - -

    (Tuckerman) Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 -(1992). -

    - diff --git a/doc/doc2/search.html b/doc/doc2/search.html deleted file mode 100644 index 112deb6952..0000000000 --- a/doc/doc2/search.html +++ /dev/null @@ -1,206 +0,0 @@ - - - - - - - - - - - Search — LAMMPS 15 May 2015 version documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    set command -

    -

    Syntax: -

    -
    set style ID keyword values ... 
-
    -
    • style = atom or type or mol or group or region - -
    • ID = atom ID range or type range or mol ID range or group ID or region ID - -
    • one or more keyword/value pairs may be appended - -
    • keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or angmom or omega or mass or density or volume or image or - bond or angle or dihedral or improper or - meso_e or meso_cv or meso_rho or smd_contact_radius or smd_mass_density or i_name or d_name - -
        type value = atom type
-    value can be an atom-style variable (see below)
-  type/fraction values = type fraction seed
-    type = new atom type
-    fraction = fraction of selected atoms to set to new atom type
-    seed = random # seed (positive integer)
-  mol value = molecule ID
-    value can be an atom-style variable (see below)
-  x,y,z value = atom coordinate (distance units)
-    value can be an atom-style variable (see below)
-  charge value = atomic charge (charge units)
-    value can be an atom-style variable (see below)
-  dipole values = x y z
-    x,y,z = orientation of dipole moment vector
-    any of x,y,z can be an atom-style variable (see below)
-  dipole/random value = seed Dlen
-    seed = random # seed (positive integer) for dipole moment orientations
-    Dlen = magnitude of dipole moment (dipole units)
-  quat values = a b c theta
-    a,b,c = unit vector to rotate particle around via right-hand rule
-    theta = rotation angle (degrees)
-    any of a,b,c,theta can be an atom-style variable (see below)
-  quat/random value = seed
-    seed = random # seed (positive integer) for quaternion orientations
-  diameter value = diameter of spherical particle (distance units)
-    value can be an atom-style variable (see below)
-  shape value = Sx Sy Sz
-    Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
-  length value = len
-    len = length of line segment (distance units)
-    len can be an atom-style variable (see below)
-  tri value = side
-    side = side length of equilateral triangle (distance units)
-    side can be an atom-style variable (see below)
-  theta value = angle (degrees)
-    angle = orientation of line segment with respect to x-axis
-    angle can be an atom-style variable (see below)
-  angmom values = Lx Ly Lz
-    Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
-    any of Lx,Ly,Lz can be an atom-style variable (see below)
-  omega values = Wx Wy Wz
-    Wx,Wy,Wz = components of angular velocity vector (radians/time units)
-    any of wx,wy,wz can be an atom-style variable (see below)
-  mass value = per-atom mass (mass units)
-    value can be an atom-style variable (see below)
-  density value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
-    value can be an atom-style variable (see below)
-  volume value = particle volume for Peridynamic particle (distance^3 units)
-    value can be an atom-style variable (see below)
-  image nx ny nz
-    nx,ny,nz = which periodic image of the simulation box the atom is in
-  bond value = bond type for all bonds between selected atoms
-  angle value = angle type for all angles between selected atoms
-  dihedral value = dihedral type for all dihedrals between selected atoms
-  improper value = improper type for all impropers between selected atoms
-  meso_e value = energy of SPH particles (need units)
-    value can be an atom-style variable (see below)
-  meso_cv value = heat capacity of SPH particles (need units)
-    value can be an atom-style variable (see below)
-  meso_rho value = density of SPH particles (need units)
-    value can be an atom-style variable (see below)
-  smd_contact_radius = radius for short range interactions, i.e. contact and friction
-    value can be an atom-style variable (see below) 
-  smd_mass_density = set particle mass based on volume by providing a mass density
-    value can be an atom-style variable (see below)
-  i_name value = value for custom integer vector with name
-  d_name value = value for custom floating-point vector with name 
-
      - -
    -

    Examples: -

    -
    set group solvent type 2
-set group solvent type/fraction 2 0.5 12393
-set group edge bond 4
-set region half charge 0.5
-set type 3 charge 0.5
-set type 1*3 charge 0.5
-set atom * charge v_atomfile
-set atom 100*200 x 0.5 y 1.0
-set atom 1492 type 3 
-
    -

    Description: -

    -

    Set one or more properties of one or more atoms. Since atom -properties are initially assigned by the read_data, -read_restart or create_atoms -commands, this command changes those assignments. This can be useful -for overriding the default values assigned by the -create_atoms command (e.g. charge = 0.0). It can -be useful for altering pairwise and molecular force interactions, -since force-field coefficients are defined in terms of types. It can -be used to change the labeling of atoms by atom type or molecule ID -when they are output in dump files. It can also be useful -for debugging purposes; i.e. positioning an atom at a precise location -to compute subsequent forces or energy. -

    -

    Note that the style and ID arguments determine which atoms have -their properties reset. The remaining keywords specify which -properties to reset and what the new values are. Some strings like -type or mol can be used as a style and/or a keyword. -

    -
    - -

    This section describes how to select which atoms to change -the properties of, via the style and ID arguments. -

    -

    The style atom selects all the atoms in a range of atom IDs. The -style type selects all the atoms in a range of types. The style -mol selects all the atoms in a range of molecule IDs. -

    -

    In each of the range cases, the range can be specified as a single -numeric value, or a wildcard asterisk can be used to specify a range -of values. This takes the form "*" or "*n" or "n*" or "m*n". For -example, for the style type, if N = the number of atom types, then -an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). For all the styles except -mol, the lowest value for the wildcard is 1; for mol it is 0. -

    -

    The style group selects all the atoms in the specified group. The -style region selects all the atoms in the specified geometric -region. See the group and region commands -for details of how to specify a group or region. -

    -
    - -

    This section describes the keyword options for which properties to -change, for the selected atoms. -

    -

    Note that except where explicitly prohibited below, all of the -keywords allow an atom-style or atomfile-style -variable to be used as the specified value(s). If the -value is a variable, it should be specified as v_name, where name is -the variable name. In this case, the variable will be evaluated, and -its resulting per-atom value used to determine the value assigned to -each selected atom. Note that the per-atom value from the variable -will be ignored for atoms that are not selected via the style and -ID settings explained above. A simple way to use per-atom values -from the variable to reset a property for all atoms is to use style -atom with ID = "*"; this selects all atom IDs. -

    -

    Atom-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters and timestep and elapsed -time. They can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a time-dependent or -spatially-dependent set of per-atom values. As explained on the -variable doc page, atomfile-style variables can be -used in place of atom-style variables, and thus as arguments to the -set command. Atomfile-style variables read their per-atoms values -from a file. -

    -

    IMPORTANT NOTE: Atom-style and atomfile-style variables return -floating point per-atom values. If the values are assigned to an -integer variable, such as the molecule ID, then the floating point -value is truncated to its integer portion, e.g. a value of 2.6 would -become 2. -

    -

    Keyword type sets the atom type for all selected atoms. The -specified value must be from 1 to ntypes, where ntypes was set by the -create_box command or the atom types field in the -header of the data file read by the read_data -command. -

    -

    Keyword type/fraction sets the atom type for a fraction of the -selected atoms. The actual number of atoms changed is not guaranteed -to be exactly the requested fraction, but should be statistically -close. Random numbers are used in such a way that a particular atom -is changed or not changed, regardless of how many processors are being -used. This keyword does not allow use of an atom-style variable. -

    -

    Keyword mol sets the molecule ID for all selected atoms. The atom -style being used must support the use of molecule -IDs. -

    -

    Keywords x, y, z, and charge set the coordinates or charge of -all selected atoms. For charge, the atom style -being used must support the use of atomic charge. -

    -

    Keyword dipole uses the specified x,y,z values as components of a -vector to set as the orientation of the dipole moment vectors of the -selected atoms. The magnitude of the dipole moment is set -by the length of this orientation vector. -

    -

    Keyword dipole/random randomizes the orientation of the dipole -moment vectors of the selected atoms and sets the magnitude of each to -the specified Dlen value. For 2d systems, the z component of the -orientation is set to 0.0. Random numbers are used in such a way that -the orientation of a particular atom is the same, regardless of how -many processors are being used. This keyword does not allow use of an -atom-style variable. -

    -

    Keyword quat uses the specified values to create a quaternion -(4-vector) that represents the orientation of the selected atoms. The -particles must be ellipsoids as defined by the atom_style -ellipsoid command or triangles as defined by the -atom_style tri command. Note that particles defined -by atom_style ellipsoid have 3 shape parameters. -The 3 values must be non-zero for each particle set by this command. -They are used to specify the aspect ratios of an ellipsoidal particle, -which is oriented by default with its x-axis along the simulation -box's x-axis, and similarly for y and z. If this body is rotated (via -the right-hand rule) by an angle theta around a unit rotation vector -(a,b,c), then the quaternion that represents its new orientation is -given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2), -c*sin(theta/2)). The theta and a,b,c values are the arguments to the -quat keyword. LAMMPS normalizes the quaternion in case (a,b,c) was -not specified as a unit vector. For 2d systems, the a,b,c values are -ignored, since a rotation vector of (0,0,1) is the only valid choice. -

    -

    Keyword quat/random randomizes the orientation of the quaternion of -the selected atoms. The particles must be ellipsoids as defined by -the atom_style ellipsoid command or triangles as -defined by the atom_style tri command. Random -numbers are used in such a way that the orientation of a particular -atom is the same, regardless of how many processors are being used. -For 2d systems, only orientations in the xy plane are generated. As -with keyword quat, for ellipsoidal particles, the 3 shape values -must be non-zero for each particle set by this command. This keyword -does not allow use of an atom-style variable. -

    -

    Keyword diameter sets the size of the selected atoms. The particles -must be finite-size spheres as defined by the atom_style -sphere command. The diameter of a particle can be -set to 0.0, which means they will be treated as point particles. Note -that this command does not adjust the particle mass, even if it was -defined with a density, e.g. via the read_data -command. -

    -

    Keyword shape sets the size and shape of the selected atoms. The -particles must be ellipsoids as defined by the atom_style -ellipsoid command. The Sx, Sy, Sz settings are -the 3 diameters of the ellipsoid in each direction. All 3 can be set -to the same value, which means the ellipsoid is effectively a sphere. -They can also all be set to 0.0 which means the particle will be -treated as a point particle. Note that this command does not adjust -the particle mass, even if it was defined with a density, e.g. via the -read_data command. -

    -

    Keyword length sets the length of selected atoms. The particles -must be line segments as defined by the atom_style -line command. If the specified value is non-zero the -line segment is (re)set to a length = the specified value, centered -around the particle position, with an orientation along the x-axis. -If the specified value is 0.0, the particle will become a point -particle. Note that this command does not adjust the particle mass, -even if it was defined with a density, e.g. via the -read_data command. -

    -

    Keyword tri sets the size of selected atoms. The particles must be -triangles as defined by the atom_style tri command. -If the specified value is non-zero the triangle is (re)set to be an -equilateral triangle in the xy plane with side length = the specified -value, with a centroid at the particle position, with its base -parallel to the x axis, and the y-axis running from the center of the -base to the top point of the triangle. If the specified value is 0.0, -the particle will become a point particle. Note that this command -does not adjust the particle mass, even if it was defined with a -density, e.g. via the read_data command. -

    -

    Keyword theta sets the orientation of selected atoms. The particles -must be line segments as defined by the atom_style -line command. The specified value is used to set the -orientation angle of the line segments with respect to the x axis. -

    -

    Keyword angmom sets the angular momentum of selected atoms. The -particles must be ellipsoids as defined by the atom_style -ellipsoid command or triangles as defined by the -atom_style tri command. The angular momentum vector -of the particles is set to the 3 specified components. -

    -

    Keyword omega sets the angular velocity of selected atoms. The -particles must be spheres as defined by the atom_style sphere -atom_style.html command. The angular velocity vector of the particles -is set to the 3 specified components. -

    -

    Keyword mass sets the mass of all selected particles. The particles -must have a per-atom mass attribute, as defined by the -atom_style command. See the "mass" command for how -to set mass values on a per-type basis. -

    -

    Keyword density also sets the mass of all selected particles, but in -a different way. The particles must have a per-atom mass attribute, -as defined by the atom_style command. If the atom -has a radius attribute (see atom_style sphere) and -its radius is non-zero, its mass is set from the density and particle -volume. If the atom has a shape attribute (see atom_style -ellipsoid) and its 3 shape parameters are non-zero, -then its mass is set from the density and particle volume. If the -atom has a length attribute (see atom_style line) -and its length is non-zero, then its mass is set from the density and -line segment length (the input density is assumed to be in -mass/distance units). If the atom has an area attribute (see -atom_style tri) and its area is non-zero, then its -mass is set from the density and triangle area (the input density is -assumed to be in mass/distance^2 units). If none of these cases are -valid, then the mass is set to the density value directly (the input -density is assumed to be in mass units). -

    -

    Keyword smd_mass_density also sets the mass of all selected -particles, but it is only applicable to the Smooth Mach Dynamics -package USER-SMD. This command assumes that the particle volume has -already been correctly set and calculates particle mass from the -provided mass density value. -

    -

    Keyword smd_contact_radius only applies to simulations with the -Smooth Mach Dynamics package USER-SMD. This command sets an -interaction radius for computing short-range interactions, -e.g. repulsive forces to prevent different individual physical bodies -from penetrating each other. Note that the SPH smoothing kernel -diameter used for computing long range, nonlocal interactions, is set -using the diameter keyword. -

    -

    Keyword volume sets the volume of all selected particles. -Currently, only the atom_style peri command defines -particles with a volume attribute. Note that this command does not -adjust the particle mass. -

    -

    Keyword image sets which image of the simulation box the atom is -considered to be in. An image of 0 means it is inside the box as -defined. A value of 2 means add 2 box lengths to get the true value. -A value of -1 means subtract 1 box length to get the true value. -LAMMPS updates these flags as atoms cross periodic boundaries during -the simulation. The flags can be output with atom snapshots via the -dump command. If a value of NULL is specified for any of -nx,ny,nz, then the current image value for that dimension is -unchanged. For non-periodic dimensions only a value of 0 can be -specified. This keyword does not allow use of atom-style variables. -This command can be useful after a system has been equilibrated and -atoms have diffused one or more box lengths in various directions. -This command can then reset the image values for atoms so that they -are effectively inside the simulation box, e.g if a diffusion -coefficient is about to be measured via the compute -msd command. Care should be taken not to reset the -image flags of two atoms in a bond to the same value if the bond -straddles a periodic boundary (rather they should be different by +/- -1). This will not affect the dynamics of a simulation, but may mess -up analysis of the trajectories if a LAMMPS diagnostic or your own -analysis relies on the image flags to unwrap a molecule which -straddles the periodic box. -

    -

    Keywords bond, angle, dihedral, and improper, set the bond -type (angle type, etc) of all bonds (angles, etc) of selected atoms to -the specified value from 1 to nbondtypes (nangletypes, etc). All -atoms in a particular bond (angle, etc) must be selected atoms in -order for the change to be made. The value of nbondtype (nangletypes, -etc) was set by the bond types (angle types, etc) field in the -header of the data file read by the read_data -command. These keywords do not allow use of an atom-style variable. -

    -

    Keywords meso_e, meso_cv, and meso_rho set the energy, heat -capacity, and density of smmothed particle hydrodynamics (SPH) -particles. See this PDF guide to -using SPH in LAMMPS. -

    -

    Keywords i_name and d_name refer to custom integer and -floating-point properties that have been added to each atom via the -fix property/atom command. When that command -is used specific names are given to each attribute which are what is -specified as the "name" portion of i_name or d_name. -

    -

    Restrictions: -

    -

    You cannot set an atom attribute (e.g. mol or q or volume) if -the atom_style does not have that attribute. -

    -

    This command requires inter-processor communication to coordinate the -setting of bond types (angle types, etc). This means that your system -must be ready to perform a simulation before using one of these -keywords (force fields set, atom mass set, etc). This is not -necessary for other keywords. -

    -

    Using the region style with the bond (angle, etc) keywords can give -unpredictable results if there are bonds (angles, etc) that straddle -periodic boundaries. This is because the region may only extend up to -the boundary and partner atoms in the bond (angle, etc) may have -coordinates outside the simulation box if they are ghost atoms. -

    -

    Related commands: -

    -

    create_box, create_atoms, -read_data -

    -

    Default: none -

    - diff --git a/doc/doc2/shell.html b/doc/doc2/shell.html deleted file mode 100644 index 0bb8b3b6d8..0000000000 --- a/doc/doc2/shell.html +++ /dev/null @@ -1,114 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    shell command -

    -

    Syntax: -

    -
    shell cmd args 
-
    -
    • cmd = cd or mkdir or mv or rm or rmdir or putenv or arbitrary command - -
        cd arg = dir
-    dir = directory to change to
-  mkdir args = dir1 dir2 ...
-    dir1,dir2 = one or more directories to create
-  mv args = old new
-    old = old filename
-    new = new filename
-  rm args = file1 file2 ...
-    file1,file2 = one or more filenames to delete
-  rmdir args = dir1 dir2 ...
-    dir1,dir2 = one or more directories to delete
-  putenv args = var1=value1 var2=value2
-    var=value = one of more definitions of environment variables
-  anything else is passed as a command to the shell for direct execution 
-
      - -
    -

    Examples: -

    -
    shell cd sub1
-shell cd ..
-shell mkdir tmp1 tmp2 tmp3
-shell rmdir tmp1
-shell mv log.lammps hold/log.1
-shell rm TMP/file1 TMP/file2
-shell putenv LAMMPS_POTENTIALS=../../potentials
-shell my_setup file1 10 file2
-shell my_post_process 100 dump.out 
-
    -

    Description: -

    -

    Execute a shell command. A few simple file-based shell commands are -supported directly, in Unix-style syntax. Any command not listed -above is passed as-is to the C-library system() call, which invokes -the command in a shell. -

    -

    This is means to invoke other commands from your input script. For -example, you can move files around in preparation for the next section -of the input script. Or you can run a program that pre-processes data -for input into LAMMPS. Or you can run a program that post-processes -LAMMPS output data. -

    -

    With the exception of cd, all commands, including ones invoked via a -system() call, are executed by only a single processor, so that -files/directories are not being manipulated by multiple processors. -

    -

    The cd cmd executes the Unix "cd" command to change the working -directory. All subsequent LAMMPS commands that read/write files will -use the new directory. All processors execute this command. -

    -

    The mkdir cmd executes the Unix "mkdir" command to create one or -more directories. -

    -

    The mv cmd executes the Unix "mv" command to rename a file and/or -move it to a new directory. -

    -

    The rm cmd executes the Unix "rm" command to remove one or more -files. -

    -

    The rmdir cmd executes the Unix "rmdir" command to remove one or -more directories. A directory must be empty to be successfully -removed. -

    -

    The putenv cmd defines or updates an environment variable directly. -Since this command does not pass through the shell, no shell variable -expansion or globbing is performed, only the usual substitution for -LAMMPS variables defined with the variable command is -performed. The resulting string is then used literally. -

    -

    Any other cmd is passed as-is to the shell along with its arguments as -one string, invoked by the C-library system() call. For example, -these lines in your input script: -

    -
    variable n equal 10
-variable foo string file2
-shell my_setup file1 $n ${foo} 
-
    -

    would be the same as invoking -

    -
    % my_setup file1 10 file2 
-
    -

    from a command-line prompt. The executable program "my_setup" is run -with 3 arguments: file1 10 file2. -

    -

    Restrictions: -

    -

    LAMMPS does not detect errors or print warnings when any of these -commands execute. E.g. if the specified directory does not exist, -executing the cd command will silently do nothing. -

    -

    Related commands: none -

    -

    Default: none -

    - diff --git a/doc/doc2/special_bonds.html b/doc/doc2/special_bonds.html deleted file mode 100644 index 58fa493988..0000000000 --- a/doc/doc2/special_bonds.html +++ /dev/null @@ -1,276 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    special_bonds command -

    -

    Syntax: -

    -
    special_bonds keyword values ... 
-
    -
    • one or more keyword/value pairs may be appended - -
    • keyword = amber or charmm or dreiding or fene or lj/coul or lj or coul or angle or dihedral or extra - -
        amber values = none
-  charmm values = none
-  dreiding values = none
-  fene values = none
-  lj/coul values = w1,w2,w3
-    w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
-  lj values = w1,w2,w3
-    w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
-  coul values = w1,w2,w3
-    w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
-  angle value = yes or no
-  dihedral value = yes or no
-  extra value = N
-    N = number of extra 1-2,1-3,1-4 interactions to save space for 
-
      - -
    -

    Examples: -

    -
    special_bonds amber
-special_bonds charmm
-special_bonds fene dihedral no
-special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
-special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
-special_bonds lj/coul 0 1 1 extra 2 
-
    -

    Description: -

    -

    Set weighting coefficients for pairwise energy and force contributions -between pairs of atoms that are also permanently bonded to each other, -either directly or via one or two intermediate bonds. These weighting -factors are used by nearly all pair styles in LAMMPS -that compute simple pairwise interactions. Permanent bonds between -atoms are specified by defining the bond topology in the data file -read by the read_data command. Typically a -bond_style command is also used to define a bond -potential. The rationale for using these weighting factors is that -the interaction between a pair of bonded atoms is all (or mostly) -specified by the bond, angle, dihedral potentials, and thus the -non-bonded Lennard-Jones or Coulombic interaction between the pair of -atoms should be excluded (or reduced by a weighting factor). -

    -

    IMPORTANT NOTE: These weighting factors are NOT used by pair -styles that compute many-body interactions, since the -"bonds" that result from such interactions are not permanent, but are -created and broken dynamically as atom conformations change. Examples -of pair styles in this category are EAM, MEAM, Stillinger-Weber, -Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no -sense to define permanent bonds between atoms that interact via these -potentials, though such bonds may exist elsewhere in your system, -e.g. when using the pair_style hybrid command. -Thus LAMMPS ignores special_bonds settings when manybody potentials -are calculated. -

    -

    IMPORTANT NOTE: Unlike some commands in LAMMPS, you cannot use this -command multiple times in an incremental fashion: e.g. to first set -the LJ settings and then the Coulombic ones. Each time you use this -command it sets all the coefficients to default values and only -overrides the one you specify, so you should set all the options you -need each time you use it. See more details at the bottom of this -page. -

    -

    The Coulomb factors are applied to any Coulomb (charge interaction) -term that the potential calculates. The LJ factors are applied to the -remaining terms that the potential calculates, whether they represent -LJ interactions or not. The weighting factors are a scaling -pre-factor on the energy and force between the pair of atoms. A value -of 1.0 means include the full interaction; a value of 0.0 means -exclude it completely. -

    -

    The 1st of the 3 coefficients (LJ or Coulombic) is the weighting -factor on 1-2 atom pairs, which are pairs of atoms directly bonded to -each other. The 2nd coefficient is the weighting factor on 1-3 atom -pairs which are those separated by 2 bonds (e.g. the two H atoms in a -water molecule). The 3rd coefficient is the weighting factor on 1-4 -atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th -atoms in a dihedral interaction). Thus if the 1-2 coefficient is set -to 0.0, then the pairwise interaction is effectively turned off for -all pairs of atoms bonded to each other. If it is set to 1.0, then -that interaction will be at full strength. -

    -

    IMPORTANT NOTE: For purposes of computing weighted pairwise -interactions, 1-3 and 1-4 interactions are not defined from the list -of angles or dihedrals used by the simulation. Rather, they are -inferred topologically from the set of bonds specified when the -simulation is defined from a data or restart file (see -read_data or read_restart -commands). Thus the set of 1-2,1-3,1-4 interactions that the weights -apply to is the same whether angle and dihedral potentials are -computed or not, and remains the same even if bonds are constrained, -or turned off, or removed during a simulation. -

    -

    The two exceptions to this rule are (a) if the angle or dihedral -keywords are set to yes (see below), or (b) if the -delete_bonds command is used with the special -option that recomputes the 1-2,1-3,1-4 topologies after bonds are -deleted; see the delete_bonds command for more -details. -

    -

    The amber keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ -interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which -is the default for a commonly used version of the AMBER force field, -where the last value is really 5/6. See (Cornell) for a -description of the AMBER force field. -

    -

    The charmm keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both -LJ and Coulombic interactions, which is the default for a commonly -used version of the CHARMM force field. Note that in pair styles -lj/charmm/coul/charmm and lj/charmm/coul/long the 1-4 coefficients -are defined explicitly, and these pairwise contributions are computed -as part of the charmm dihedral style - see the -pair_coeff and dihedral_style -commands for more information. See (MacKerell) for a -description of the CHARMM force field. -

    -

    The dreiding keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both -LJ and Coulombic interactions, which is the default for the Dreiding -force field, as discussed in (Mayo). -

    -

    The fene keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both -LJ and Coulombic interactions, which is consistent with a -coarse-grained polymer model with FENE bonds. See -(Kremer) for a description of FENE bonds. -

    -

    The lj/coul, lj, and coul keywords allow the 3 coefficients to -be set explicitly. The lj/coul keyword sets both the LJ and -Coulombic coefficients to the same 3 values. The lj and coul -keywords only set either the LJ or Coulombic coefficients. Use both -of them if you wish to set the LJ coefficients to different values -than the Coulombic coefficients. -

    -

    The angle keyword allows the 1-3 weighting factor to be ignored for -individual atom pairs if they are not listed as the first and last -atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in -any dihedral defined in the simulation. For example, imagine the 1-3 -weighting factor is set to 0.5 and you have a linear molecule with 4 -atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3 -as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a -dihedral, then the pairwise interaction between atoms 1 and 3 will -always be weighted by 0.5, but different force fields use different -rules for weighting the pairwise interaction between atoms 2 and 4. -If the angle keyword is specified as yes, then the pairwise -interaction between atoms 2 and 4 will be unaffected (full weighting -of 1.0). If the angle keyword is specified as no which is the -default, then the 2,4 interaction will also be weighted by 0.5. -

    -

    The dihedral keyword allows the 1-4 weighting factor to be ignored -for individual atom pairs if they are not listed as the first and last -atoms in any dihedral defined in the simulation. For example, imagine -the 1-4 weighting factor is set to 0.5 and you have a linear molecule -with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file -defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a -dihedral, then the pairwise interaction between atoms 1 and 4 will -always be weighted by 0.5, but different force fields use different -rules for weighting the pairwise interaction between atoms 2 and 5. -If the dihedral keyword is specified as yes, then the pairwise -interaction between atoms 2 and 5 will be unaffected (full weighting -of 1.0). If the dihedral keyword is specified as no which is the -default, then the 2,5 interaction will also be weighted by 0.5. -

    -

    The extra keyword can be used when additional bonds will be created -during a simulation run, e.g. by the fix -bond/create command. It can also be used if -molecules will be added to the system, e.g. via the fix -deposit, or fix pour commands, which -will have atoms with more special neighbors than any atom in the -current system has. -

    -
    - -

    IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a -list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond -topology of the system). If new bonds are created (or molecules added -containing atoms with more special neighbors), the size of this list -needs to grow. Note that adding a single bond always adds a new 1st -neighbor but may also induce *many* new 2nd and 3rd neighbors, -depending on the molecular topology of your system. Using the extra -keyword leaves empty space in the list for this N additional 1st, 2nd, -or 3rd neighbors to be added. If you do not do this, you may get an -error when bonds (or molecules) are added. -

    -
    - -

    IMPORTANT NOTE: If you reuse this command in an input script, you -should set all the options you need each time. This command cannot be -used a 2nd time incrementally, e.g. to add some extra storage -locations via the extra keyword. E.g. these two commands: -

    -

    special_bonds lj 0.0 1.0 1.0 -special_bonds coul 0.0 0.0 1.0 -

    -

    are not the same as -

    -

    special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0 -

    -

    In the first case you end up with (after the 2nd command): -

    -

    LJ: 0.0 0.0 0.0 -Coul: coul 0.0 0.0 1.0 -

    -

    because the LJ settings are reset to their default values -each time the command is issued. -

    -

    Likewise -

    -
    special_bonds amber
-special_bonds extra 2 
-
    -

    is not the same as this single command: -

    -
    special_bonds amber extra 2 
-
    -

    since in the former case, the 2nd command will reset all the LJ and -Coulombic weights to 0.0 (the default). -

    -

    One exception to this rule is the extra option itself. It is not -reset to its default value of 0 each time the special_bonds command is -invoked. This is because it can also be set by the -read_data and create_box commands, -so this command will not override those settings unless you explicitly -use extra as an option. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    delete_bonds, fix bond/create -

    -

    Default: -

    -

    All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0, -angle = no, dihedral = no, and extra = 0. -

    -
    - - - -

    (Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). -

    - - -

    (Kremer) Kremer, Grest, J Chem Phys, 92, 5057 (1990). -

    - - -

    (MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). -

    - - -

    (Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). -

    - diff --git a/doc/doc2/suffix.html b/doc/doc2/suffix.html deleted file mode 100644 index bc8cc55424..0000000000 --- a/doc/doc2/suffix.html +++ /dev/null @@ -1,111 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    suffix command -

    -

    Syntax: -

    -
    suffix style args 
-
    -
    • style = off or on or cuda or gpu or intel or kk or omp or opt or hybrid -
    • args = for hybrid style, default suffix to be used and alternative suffix -
    -

    Examples: -

    -
    suffix off
-suffix on
-suffix gpu
-suffix intel
-suffix hybrid intel omp
-suffix kk 
-
    -

    Description: -

    -

    This command allows you to use variants of various styles if they -exist. In that respect it operates the same as the -suffix -command-line switch. It also has options -to turn off or back on any suffix setting made via the command line. -

    -

    The specified style can be cuda, gpu, intel, kk, omp, opt -or hybrid. These refer to optional packages that LAMMPS can be built -with, as described in this section of the -manual. The "cuda" style corresponds to -the USER-CUDA package, the "gpu" style to the GPU package, the "intel" -style to the USER-INTEL package, the "kk" style to the KOKKOS package, -the "omp" style to the USER-OMP package, and the "opt" style to the -OPT package. -

    -

    These are the variants these packages provide: -

    -
    • USER-CUDA = a collection of atom, pair, fix, compute, and intergrate -styles, optimized to run on one or more NVIDIA GPUs - -
    • GPU = a handful of pair styles and the PPPM kspace_style, optimized to -run on one or more GPUs or multicore CPU/GPU nodes - -
    • USER-INTEL = a collection of pair styles and neighbor routines -optimized to run in single, mixed, or double precision on CPUs and -Intel(R) Xeon Phi(TM) coprocessors. - -
    • KOKKOS = a collection of atom, pair, and fix styles optimized to run -using the Kokkos library on various kinds of hardware, including GPUs -via Cuda and many-core chips via OpenMP or threading. - -
    • USER-OMP = a collection of pair, bond, angle, dihedral, improper, -kspace, compute, and fix styles with support for OpenMP -multi-threading - -
    • OPT = a handful of pair styles, cache-optimized for faster CPU -performance - -
    • HYBRID = a combination of two packages can be specified (see below) -
    -

    As an example, all of the packages provide a pair_style -lj/cut variant, with style names lj/cut/opt, lj/cut/omp, -lj/cut/gpu, lj/cut/intel, lj/cut/cuda, or lj/cut/kk. A variant styles -can be specified explicitly in your input script, e.g. pair_style -lj/cut/gpu. If the suffix command is used with the appropriate style, -you do not need to modify your input script. The specified suffix -(opt,omp,gpu,intel,cuda,kk) is automatically appended whenever your -input script command creates a new atom, -pair, bond, -angle, dihedral, -improper, kspace, -fix, compute, or run style. -If the variant version does not exist, the standard version is -created. -

    -

    For "hybrid", two packages are specified. The first is used whenever -available. If a style with the first suffix is not available, the style -with the suffix for the second package will be used if available. For -example, "hybrid intel omp" will use styles from the USER-INTEL package -as a first choice and styles from the USER-OMP package as a second choice -if no USER-INTEL variant is available. -

    -

    If the specified style is off, then any previously specified suffix -is temporarily disabled, whether it was specified by a command-line -switch or a previous suffix command. If the specified style is on, -a disabled suffix is turned back on. The use of these 2 commands lets -your input script use a standard LAMMPS style (i.e. a non-accelerated -variant), which can be useful for testing or benchmarking purposes. -Of course this is also possible by not using any suffix commands, and -explictly appending or not appending the suffix to the relevant -commands in your input script. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    Command-line switch -suffix -

    -

    Default: none -

    - diff --git a/doc/doc2/tad.html b/doc/doc2/tad.html deleted file mode 100644 index b3e0982342..0000000000 --- a/doc/doc2/tad.html +++ /dev/null @@ -1,327 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    tad command -

    -

    Syntax: -

    -
    tad N t_event T_lo T_hi delta tmax compute-ID keyword value ... 
-
    -
    • N = # of timesteps to run (not including dephasing/quenching) - -
    • t_event = timestep interval between event checks - -
    • T_lo = temperature at which event times are desired - -
    • T_hi = temperature at which MD simulation is performed - -
    • delta = desired confidence level for stopping criterion - -
    • tmax = reciprocal of lowest expected preexponential factor (time units) - -
    • compute-ID = ID of the compute used for event detection - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = min or neb or min_style or neb_style or neb_log - -
        min values = etol ftol maxiter maxeval
-    etol = stopping tolerance for energy (energy units)
-    ftol = stopping tolerance for force (force units)
-    maxiter = max iterations of minimize
-    maxeval = max number of force/energy evaluations
-  neb values = ftol N1 N2 Nevery
-    etol = stopping tolerance for energy (energy units)
-    ftol = stopping tolerance for force (force units)
-    N1 = max # of iterations (timesteps) to run initial NEB 
-    N2 = max # of iterations (timesteps) to run barrier-climbing NEB
-    Nevery = print NEB statistics every this many timesteps
-  neb_style value = quickmin or fire
-  neb_step value = dtneb
-    dtneb = timestep for NEB damped dynamics minimization
-  neb_log value = file where NEB statistics are printed 
-
      - -
    -

    Examples: -

    -
    tad 2000 50 1800 2300 0.01 0.01 event
-tad 2000 50 1800 2300 0.01 0.01 event &
-    min 1e-05 1e-05 100 100 &
-    neb 0.0 0.01 200 200 20 &
-    min_style cg &
-    neb_style fire &
-    neb_log log.neb 
-
    -

    Description: -

    -

    Run a temperature accelerated dynamics (TAD) simulation. This method -requires two or more partitions to perform NEB transition state -searches. -

    -

    TAD is described in this paper by Art Voter. It is a method -that uses accelerated dynamics at an elevated temperature to generate -results at a specified lower temperature. A good overview of -accelerated dynamics methods for such systems is given in this review -paper from the same group. In general, these methods assume -that the long-time dynamics is dominated by infrequent events i.e. the -system is is confined to low energy basins for long periods, -punctuated by brief, randomly-occurring transitions to adjacent -basins. TAD is suitable for infrequent-event systems, where in -addition, the transition kinetics are well-approximated by harmonic -transition state theory (hTST). In hTST, the temperature dependence of -transition rates follows the Arrhenius relation. As a consequence a -set of event times generated in a high-temperature simulation can be -mapped to a set of much longer estimated times in the low-temperature -system. However, because this mapping involves the energy barrier of -the transition event, which is different for each event, the first -event at the high temperature may not be the earliest event at the low -temperature. TAD handles this by first generating a set of possible -events from the current basin. After each event, the simulation is -reflected backwards into the current basin. This is repeated until -the stopping criterion is satisfied, at which point the event with the -earliest low-temperature occurrence time is selected. The stopping -criterion is that the confidence measure be greater than -1-delta. The confidence measure is the probability that no earlier -low-temperature event will occur at some later time in the -high-temperature simulation. hTST provides an lower bound for this -probability, based on the user-specified minimum pre-exponential -factor (reciprocal of tmax). -

    -

    In order to estimate the energy barrier for each event, the TAD method -invokes the NEB method. Each NEB replica runs on a -partition of processors. The current NEB implementation in LAMMPS -restricts you to having exactly one processor per replica. For more -information, see the documentation for the neb command. In -the current LAMMPS implementation of TAD, all the non-NEB TAD -operations are performed on the first partition, while the other -partitions remain idle. See Section_howto -5 of the manual for further discussion of -multi-replica simulations. -

    -

    A TAD run has several stages, which are repeated each time an event is -performed. The logic for a TAD run is as follows: -

    -
    while (time remains):
-  while (time < tstop):
-    until (event occurs):
-      run dynamics for t_event steps
-      quench
-    run neb calculation using all replicas
-    compute tlo from energy barrier
-    update earliest event
-    update tstop
-    reflect back into current basin
-  execute earliest event 
-
    -

    Before this outer loop begins, the initial potential energy basin is -identified by quenching (an energy minimization, see below) the -initial state and storing the resulting coordinates for reference. -

    -

    Inside the inner loop, dynamics is run continuously according to -whatever integrator has been specified by the user, stopping every -t_event steps to check if a transition event has occurred. This -check is performed by quenching the system and comparing the resulting -atom coordinates to the coordinates from the previous basin. -

    -

    A quench is an energy minimization and is performed by whichever -algorithm has been defined by the min_style command; -its default is the CG minimizer. The tolerances and limits for each -quench can be set by the min keyword. Note that typically, you do -not need to perform a highly-converged minimization to detect a -transition event. -

    -

    The event check is performed by a compute with the specified -compute-ID. Currently there is only one compute that works with the -TAD commmand, which is the compute -event/displace command. Other -event-checking computes may be added. Compute -event/displace checks whether any atom in -the compute group has moved further than a specified threshold -distance. If so, an "event" has occurred. -

    -

    The NEB calculation is similar to that invoked by the neb -command, except that the final state is generated internally, instead -of being read in from a file. The style of minimization performed by -NEB is determined by the neb_style keyword and must be a damped -dynamics minimizer. The tolerances and limits for each NEB -calculation can be set by the neb keyword. As discussed on the -neb, it is often advantageous to use a larger timestep for -NEB than for normal dyanmics. Since the size of the timestep set by -the timestep command is used by TAD for performing -dynamics, there is a neb_step keyword which can be used to set a -larger timestep for each NEB calculation if desired. -

    -
    - -

    A key aspect of the TAD method is setting the stopping criterion -appropriately. If this criterion is too conservative, then many -events must be generated before one is finally executed. Conversely, -if this criterion is too aggressive, high-entropy high-barrier events -will be over-sampled, while low-entropy low-barrier events will be -under-sampled. If the lowest pre-exponential factor is known fairly -accurately, then it can be used to estimate tmax, and the value of -delta can be set to the desired confidence level e.g. delta = 0.05 -corresponds to 95% confidence. However, for systems where the dynamics -are not well characterized (the most common case), it will be -necessary to experiment with the values of delta and tmax to get a -good trade-off between accuracy and performance. -

    -

    A second key aspect is the choice of t_hi. A larger value greatly -increases the rate at which new events are generated. However, too -large a value introduces errors due to anharmonicity (not accounted -for within hTST). Once again, for any given system, experimentation is -necessary to determine the best value of t_hi. -

    -
    - -

    Five kinds of output can be generated during a TAD run: event -statistics, NEB statistics, thermodynamic output by each replica, dump -files, and restart files. -

    -

    Event statistics are printed to the screen and master log.lammps file -each time an event is executed. The quantities are the timestep, CPU -time, global event number N, local event number M, event status, -energy barrier, time margin, t_lo and delt_lo. The timestep is -the usual LAMMPS timestep, which corresponds to the high-temperature -time at which the event was detected, in units of timestep. The CPU -time is the total processor time since the start of the TAD run. The -global event number N is a counter that increments with each -executed event. The local event number M is a counter that resets to -zero upon entering each new basin. The event status is E when an -event is executed, and is D for an event that is detected, while -DF is for a detected event that is also the earliest (first) event -at the low temperature. -

    -

    The time margin is the ratio of the high temperature time in the -current basin to the stopping time. This last number can be used to -judge whether the stopping time is too short or too long (see above). -

    -

    t_lo is the low-temperature event time when the current basin was -entered, in units of timestep. delt_lo is the time of each detected -event, measured relative to t_lo. delt_lo is equal to the -high-temperature time since entering the current basin, scaled by an -exponential factor that depends on the hi/lo temperature ratio and the -energy barrier for that event. -

    -

    On lines for executed events, with status E, the global event number -is incremented by one, -the local event number and time margin are reset to zero, -while the global event number, energy barrier, and -delt_lo match the last event with status DF -in the immediately preceding block of detected events. -The low-temperature event time t_lo is incremented by delt_lo. -

    -

    NEB statistics are written to the file specified by the neb_log -keyword. If the keyword value is "none", then no NEB statistics are -printed out. The statistics are written every Nevery timesteps. See -the neb command for a full description of the NEB -statistics. When invoked from TAD, NEB statistics are never printed to -the screen. -

    -

    Because the NEB calculation must run on multiple partitions, LAMMPS -produces additional screen and log files for each partition, -e.g. log.lammps.0, log.lammps.1, etc. For the TAD command, these -contain the thermodynamic output of each NEB replica. In addition, the -log file for the first partition, log.lammps.0, will contain -thermodynamic output from short runs and minimizations corresponding -to the dynamics and quench operations, as well as a line for each new -detected event, as described above. -

    -

    After the TAD command completes, timing statistics for the TAD run are -printed in each replica's log file, giving a breakdown of how much CPU -time was spent in each stage (NEB, dynamics, quenching, etc). -

    -

    Any dump files defined in the input script will be written -to during a TAD run at timesteps when an event is executed. This -means the the requested dump frequency in the dump command -is ignored. There will be one dump file (per dump command) created -for all partitions. The atom coordinates of the dump snapshot are -those of the minimum energy configuration resulting from quenching -following the executed event. The timesteps written into the dump -files correspond to the timestep at which the event occurred and NOT -the clock. A dump snapshot corresponding to the initial minimum state -used for event detection is written to the dump file at the beginning -of each TAD run. -

    -

    If the restart command is used, a single restart file -for all the partitions is generated, which allows a TAD run to be -continued by a new input script in the usual manner. The restart file -is generated after an event is executed. The restart file contains a -snapshot of the system in the new quenched state, including the event -number and the low-temperature time. The restart frequency specified -in the restart command is interpreted differently when -performing a TAD run. It does not mean the timestep interval between -restart files. Instead it means an event interval for executed -events. Thus a frequency of 1 means write a restart file every time -an event is executed. A frequency of 10 means write a restart file -every 10th executed event. When an input script reads a restart file -from a previous TAD run, the new script can be run on a different -number of replicas or processors. -

    -

    Note that within a single state, the dynamics will typically -temporarily continue beyond the event that is ultimately chosen, until -the stopping criterionis satisfied. When the event is eventually -executed, the timestep counter is reset to the value when the event -was detected. Similarly, after each quench and NEB minimization, the -timestep counter is reset to the value at the start of the -minimization. This means that the timesteps listed in the replica log -files do not always increase monotonically. However, the timestep -values printed to the master log file, dump files, and restart files -are always monotonically increasing. -

    -
    - -

    Restrictions: -

    -

    This command can only be used if LAMMPS was built with the REPLICA -package. See the Making LAMMPS section -for more info on packages. -

    -

    N setting must be integer multiple of t_event. -

    -

    Runs restarted from restart files written during a TAD run will only -produce identical results if the user-specified integrator supports -exact restarts. So fix nvt will produce an exact -restart, but fix langevin will not. -

    -

    This command cannot be used when any fixes are defined that keep track -of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as fix -ave/spatial. Also fix -dt/reset and fix deposit. -

    -

    Related commands: -

    -

    compute event/displace, -min_modify, min_style, -run_style, minimize, -temper, neb, -prd -

    -

    Default: -

    -

    The option defaults are min = 0.1 0.1 40 50, neb = 0.01 100 100 -10, neb_style = quickmin, neb_step = the same timestep set by -the timestep command, and neb_log = "none". -

    -
    - - - -

    (Voter) Sorensen and Voter, J Chem Phys, 112, 9599 (2000) -

    - - -

    (Voter2) Voter, Montalenti, Germann, Annual Review of Materials -Research 32, 321 (2002). -

    - diff --git a/doc/doc2/temper.html b/doc/doc2/temper.html deleted file mode 100644 index 6523d13037..0000000000 --- a/doc/doc2/temper.html +++ /dev/null @@ -1,137 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    temper command -

    -

    Syntax: -

    -
    temper N M temp fix-ID seed1 seed2 index 
-
    -
    • N = total # of timesteps to run -
    • M = attempt a tempering swap every this many steps -
    • temp = initial temperature for this ensemble -
    • fix-ID = ID of the fix that will control temperature during the run -
    • seed1 = random # seed used to decide on adjacent temperature to partner with -
    • seed2 = random # seed for Boltzmann factor in Metropolis swap -
    • index = which temperature (0 to N-1) I am simulating (optional) -
    -

    Examples: -

    -
    temper 100000 100 $t tempfix 0 58728
-temper 40000 100 $t tempfix 0 32285 $w 
-
    -

    Description: -

    -

    Run a parallel tempering or replica exchange simulation using multiple -replicas (ensembles) of a system. Two or more replicas must be used. -

    -

    Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the -partition command-line -switch; see Section_start 6 of the -manual. Note that if you have MPI installed, you can run a -multi-replica simulation with more replicas (partitions) than you have -physical processors, e.g you can run a 10-replica simulation on one or -two processors. You will simply not get the performance speed-up you -would see with one or more physical processors per replica. See this -section of the manual for further -discussion. -

    -

    Each replica's temperature is controlled at a different value by a fix -with fix-ID that controls temperature. Possible fix styles are -nvt, temp/berendsen, -langevin and temp/rescale. -The desired temperature is specified by temp, which is typically a -variable previously set in the input script, so that each partition is -assigned a different temperature. See the variable -command for more details. For example: -

    -
    variable t world 300.0 310.0 320.0 330.0
-fix myfix all nvt temp $t $t 100.0
-temper 100000 100 $t myfix 3847 58382 
-
    -

    would define 4 temperatures, and assign one of them to the thermostat -used by each replica, and to the temper command. -

    -

    As the tempering simulation runs for N timesteps, a temperature swap -between adjacent ensembles will be attempted every M timesteps. If -seed1 is 0, then the swap attempts will alternate between odd and -even pairings. If seed1 is non-zero then it is used as a seed in a -random number generator to randomly choose an odd or even pairing each -time. Each attempted swap of temperatures is either accepted or -rejected based on a Boltzmann-weighted Metropolis criterion which uses -seed2 in the random number generator. -

    -

    As a tempering run proceeds, multiple log files and screen output -files are created, one per replica. By default these files are named -log.lammps.M and screen.M where M is the replica number from 0 to N-1, -with N = # of replicas. See the section on command-line -switches for info on how to change these -names. -

    -

    The main screen and log file (log.lammps) will list information about -which temperature is assigned to each replica at each thermodynamic -output timestep. E.g. for a simulation with 16 replicas: -

    -
    Running on 16 partitions of processors
-Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
-0    0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
-500  1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
-1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
-1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
-2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
-2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
-... 
-
    -

    The column headings T0 to TN-1 mean which temperature is currently -assigned to the replica 0 to N-1. Thus the columns represent replicas -and the value in each column is its temperature (also numbered 0 to -N-1). For example, a 0 in the 4th column (column T3, step 2500) means -that the 4th replica is assigned temperature 0, i.e. the lowest -temperature. You can verify this time sequence of temperature -assignments for the Nth replica by comparing the Nth column of screen -output to the thermodynamic data in the corresponding log.lammps.N or -screen.N files as time proceeds. -

    -

    The last argument index in the temper command is optional and is -used when restarting a tempering run from a set of restart files (one -for each replica) which had previously swapped to new temperatures. -The index value (from 0 to N-1, where N is the # of replicas) -identifies which temperature the replica was simulating on the -timestep the restart files were written. Obviously, this argument -must be a variable so that each partition has the correct value. Set -the variable to the N values listed in the log file for the previous -run for the replica temperatures at that timestep. For example if the -log file listed the following for a simulation with 5 replicas: -

    -
    500000 2 4 0 1 3 
-
    -

    then a setting of -

    -
    variable w world 2 4 0 1 3 
-
    -

    would be used to restart the run with a tempering command like the -example above with $w as the last argument. -

    -
    - -

    Restrictions: -

    -

    This command can only be used if LAMMPS was built with the REPLICA -package. See the Making LAMMPS section -for more info on packages. -

    -

    Related commands: -

    -

    variable, prd, neb -

    -

    Default: none -

    - diff --git a/doc/doc2/thermo.html b/doc/doc2/thermo.html deleted file mode 100644 index aa36e9eb56..0000000000 --- a/doc/doc2/thermo.html +++ /dev/null @@ -1,64 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    thermo command -

    -

    Syntax: -

    -
    thermo N 
-
    -
    • N = output thermodynamics every N timesteps -
    • N can be a variable (see below) -
    -

    Examples: -

    -
    thermo 100 
-
    -

    Description: -

    -

    Compute and print thermodynamic info (e.g. temperature, energy, -pressure) on timesteps that are a multiple of N and at the beginning -and end of a simulation. A value of 0 will only print thermodynamics -at the beginning and end. -

    -

    The content and format of what is printed is controlled by the -thermo_style and -thermo_modify commands. -

    -

    Instead of a numeric value, N can be specifed as an equal-style -variable, which should be specified as v_name, where -name is the variable name. In this case, the variable is evaluated at -the beginning of a run to determine the next timestep at which -thermodynamic info will be written out. On that timestep, the -variable will be evaluated again to determine the next timestep, etc. -Thus the variable should return timestep values. See the stagger() -and logfreq() and stride() math functions for equal-style -variables, as examples of useful functions to use in -this context. Other similar math functions could easily be added as -options for equal-style variables. -

    -

    For example, the following commands will output thermodynamic info at -timesteps 0,10,20,30,100,200,300,1000,2000,etc: -

    -
    variable	s equal logfreq(10,3,10)
-thermo	        v_s 
-
    -

    Restrictions: none -

    -

    Related commands: -

    -

    thermo_style, thermo_modify -

    -

    Default: -

    -
    thermo 0 
-
    - diff --git a/doc/doc2/thermo_modify.html b/doc/doc2/thermo_modify.html deleted file mode 100644 index 5d2b90f230..0000000000 --- a/doc/doc2/thermo_modify.html +++ /dev/null @@ -1,173 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    thermo_modify command -

    -

    Syntax: -

    -
    thermo_modify keyword value ... 
-
    -
    • one or more keyword/value pairs may be listed - -
      keyword = lost or lost/bond or norm or flush or line or format or temp or press:l
-  lost value = error or warn or ignore
-  lost/bond value = error or warn or ignore
-  norm value = yes or no
-  flush value = yes or no
-  line value = one or multi
-  format values = int string or float string or M string
-    M = integer from 1 to N, where N = # of quantities being printed
-    string = C-style format string
-  temp value = compute ID that calculates a temperature
-  press value = compute ID that calculates a pressure 
-
      - -
    -

    Examples: -

    -
    thermo_modify lost ignore flush yes
-thermo_modify temp myTemp format 3 %15.8g
-thermo_modify line multi format float %g 
-
    -

    Description: -

    -

    Set options for how thermodynamic information is computed and printed -by LAMMPS. -

    -

    IMPORTANT NOTE: These options apply to the currently defined thermo -style. When you specify a thermo_style command, -all thermodynamic settings are restored to their default values, -including those previously reset by a thermo_modify command. Thus if -your input script specifies a thermo_style command, you should use the -thermo_modify command after it. -

    -

    The lost keyword determines whether LAMMPS checks for lost atoms -each time it computes thermodynamics and what it does if atoms are -lost. An atom can be "lost" if it moves across a non-periodic -simulation box boundary or if it moves more than a box -length outside the simulation domain (or more than a processor -sub-domain length) before reneighboring occurs. The latter case is -typically due to bad dynamics, e.g. too large a timestep or huge -forces and velocities. If the value is ignore, LAMMPS does not -check for lost atoms. If the value is error or warn, LAMMPS -checks and either issues an error or warning. The code will exit with -an error and continue with a warning. A warning will only be issued -once, the first time an atom is lost. This can be a useful debugging -option. -

    -

    The lost/bond keyword determines whether LAMMPS throws an error or -not if an atom in a bonded interaction (bond, angle, etc) cannot be -found when it creates bonded neighbor lists. By default this is a -fatal error. However in some scenarios it may be desirable to only -issue a warning or ignore it and skip the computation of the missing -bond, angle, etc. An example would be when gas molecules in a vapor -are drifting out of the box through a fixed boundary condition (see -the boundary command). In this case one atom may be -deleted before the rest of the molecule is, on a later timestep. -

    -

    The norm keyword determines whether various thermodynamic output -values are normalized by the number of atoms or not, depending on -whether it is set to yes or no. Different unit styles have -different defaults for this setting (see below). Even if norm is -set to yes, a value is only normalized if it is an "extensive" -quantity, meaning that it scales with the number of atoms in the -system. For the thermo keywords described by the doc page for the -thermo_style command, all energy-related keywords -are extensive, such as pe or ebond or enthalpy. Other keywords -such as temp or press are "intensive" meaning their value is -independent (in a statistical sense) of the number of atoms in the -system and thus are never normalized. For thermodynamic output values -extracted from fixes and computes in a thermo_style -custom command, the doc page for the individual -fix or compute lists whether the value is -"extensive" or "intensive" and thus whether it is normalized. -Thermodynamic output values calculated by a variable formula are -assumed to be "intensive" and thus are never normalized. You can -always include a divide by the number of atoms in the variable formula -if this is not the case. -

    -

    The flush keyword invokes a flush operation after thermodynamic info -is written to the log file. This insures the output in that file is -current (no buffering by the OS), even if LAMMPS halts before the -simulation completes. -

    -

    The line keyword determines whether thermodynamics will be printed -as a series of numeric values on one line or in a multi-line format -with 3 quantities with text strings per line and a dashed-line header -containing the timestep and CPU time. This modify option overrides -the one and multi thermo_style settings. -

    -

    The format keyword sets the numeric format of individual printed -quantities. The int and float keywords set the format for all -integer or floating-point quantities printed. The setting with a -numeric value M (e.g. format 5 %10.4g) sets the format of the Mth -value printed in each output line, e.g. the 5th column of output in -this case. If the format for a specific column has been set, it will -take precedent over the int or float setting. -

    -

    IMPORTANT NOTE: The thermo output values step and atoms are stored -internally as 8-byte signed integers, rather than the usual 4-byte -signed integers. When specifying the "format int" keyword you can use -a "%d"-style format identifier in the format string and LAMMPS will -convert this to the corresponding "%lu" form when it is applied to -those keywords. However, when specifying the "format M string" -keyword for step and natoms, you should specify a string -appropriate for an 8-byte signed integer, e.g. one with "%ld". -

    -

    The temp keyword is used to determine how thermodynamic temperature -is calculated, which is used by all thermo quantities that require a -temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc). -The specified compute ID must have been previously defined by the user -via the compute command and it must be a style of -compute that calculates a temperature. As described in the -thermo_style command, thermo output uses a default -compute for temperature with ID = thermo_temp. This option allows -the user to override the default. -

    -

    The press keyword is used to determine how thermodynamic pressure is -calculated, which is used by all thermo quantities that require a -pressure ("press", "enthalpy", "pxx", etc). The specified compute ID -must have been previously defined by the user via the -compute command and it must be a style of compute that -calculates a pressure. As described in the -thermo_style command, thermo output uses a default -compute for pressure with ID = thermo_press. This option allows the -user to override the default. -

    -

    IMPORTANT NOTE: If both the temp and press keywords are used in a -single thermo_modify command (or in two separate commands), then the -order in which the keywords are specified is important. Note that a -pressure compute defines its own temperature -compute as an argument when it is specified. The temp keyword will -override this (for the pressure compute being used by thermodynamics), -but only if the temp keyword comes after the press keyword. If -the temp keyword comes before the press keyword, then the new -pressure compute specified by the press keyword will be unaffected -by the temp setting. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    thermo, thermo_style -

    -

    Default: -

    -

    The option defaults are lost = error, norm = yes for unit style of -lj, norm = no for unit style of real and metal, flush = no, -and temp/press = compute IDs defined by thermo_style. -

    -

    The defaults for the line and format options depend on the thermo -style. For styles "one" and "custom", the line and format defaults -are "one", "%8d", and "%12.8g". For style "multi", the line and -format defaults are "multi", "%8d", and "%14.4f". -

    - diff --git a/doc/doc2/thermo_style.html b/doc/doc2/thermo_style.html deleted file mode 100644 index 593ba371f8..0000000000 --- a/doc/doc2/thermo_style.html +++ /dev/null @@ -1,371 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    thermo_style command -

    -

    Syntax: -

    -
    thermo_style style args 
-
    -
    • style = one or multi or custom - -
    • args = list of arguments for a particular style - -
        one args = none
-  multi args = none
-  custom args = list of keywords
-    possible keywords = step, elapsed, elaplong, dt, time,
-                        cpu, tpcpu, spcpu, cpuremain, part,
-                        atoms, temp, press, pe, ke, etotal, enthalpy,
-                        evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
-                        emol, elong, etail,
-                        vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
-		        xy, xz, yz, xlat, ylat, zlat,
-                        bonds, angles, dihedrals, impropers,
-		        pxx, pyy, pzz, pxy, pxz, pyz,
-			fmax, fnorm, nbuild, ndanger,
-			cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
-			c_ID, c_ID[I], c_ID[I][J],
-                        f_ID, f_ID[I], f_ID[I][J],
-                        v_name
-      step = timestep
-      elapsed = timesteps since start of this run
-      elaplong = timesteps since start of initial run in a series of runs
-      dt = timestep size
-      time = simulation time
-      cpu = elapsed CPU time in seconds
-      tpcpu = time per CPU second
-      spcpu = timesteps per CPU second
-      cpuremain = estimated CPU time remaining in run
-      part = which partition (0 to Npartition-1) this is
-      atoms = # of atoms
-      temp = temperature
-      press = pressure
-      pe = total potential energy
-      ke = kinetic energy
-      etotal = total energy (pe + ke)
-      enthalpy = enthalpy (etotal + press*vol)
-      evdwl = VanderWaal pairwise energy
-      ecoul = Coulombic pairwise energy
-      epair = pairwise energy (evdwl + ecoul + elong + etail)
-      ebond = bond energy
-      eangle = angle energy
-      edihed = dihedral energy
-      eimp = improper energy
-      emol = molecular energy (ebond + eangle + edihed + eimp)
-      elong = long-range kspace energy
-      etail = VanderWaal energy long-range tail correction
-      vol = volume
-      density = mass density of system
-      lx,ly,lz = box lengths in x,y,z
-      xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
-      xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
-      xlat,ylat,zlat = lattice spacings as calculated by lattice command
-      bonds,angles,dihedrals,impropers = # of these interactions defined
-      pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
-      fmax = max component of force on any atom in any dimension
-      fnorm = length of force vector for all atoms
-      nbuild = # of neighbor list builds
-      ndanger = # of dangerous neighbor list builds
-      cella,cellb,cellc = periodic cell lattice constants a,b,c 
-      cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
-      c_ID = global scalar value calculated by a compute with ID
-      c_ID[I] = Ith component of global vector calculated by a compute with ID
-      c_ID[I][J] = I,J component of global array calculated by a compute with ID
-      f_ID = global scalar value calculated by a fix with ID
-      f_ID[I] = Ith component of global vector calculated by a fix with ID
-      f_ID[I][J] = I,J component of global array calculated by a fix with ID
-      v_name = scalar value calculated by an equal-style variable with name 
-
      - -
    -

    Examples: -

    -
    thermo_style multi
-thermo_style custom step temp pe etotal press vol
-thermo_style custom step temp etotal c_myTemp v_abc 
-
    -

    Description: -

    -

    Set the style and content for printing thermodynamic data to the -screen and log file. -

    -

    Style one prints a one-line summary of thermodynamic info that is -the equivalent of "thermo_style custom step temp epair emol etotal -press". The line contains only numeric values. -

    -

    Style multi prints a multiple-line listing of thermodynamic info -that is the equivalent of "thermo_style custom etotal ke temp pe ebond -eangle edihed eimp evdwl ecoul elong press". The listing contains -numeric values and a string ID for each quantity. -

    -

    Style custom is the most general setting and allows you to specify -which of the keywords listed above you want printed on each -thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are -references to computes, fixes, and -equal-style variables that have been defined -elsewhere in the input script or can even be new styles which users -have added to LAMMPS (see the Section_modify -section of the documentation). Thus the custom style provides a -flexible means of outputting essentially any desired quantity as a -simulation proceeds. -

    -

    All styles except custom have vol appended to their list of -outputs if the simulation box volume changes during the simulation. -

    -

    The values printed by the various keywords are instantaneous values, -calculated on the current timestep. Time-averaged quantities, which -include values from previous timesteps, can be output by using the -f_ID keyword and accessing a fix that does time-averaging such as the -fix ave/time command. -

    -

    Options invoked by the thermo_modify command can -be used to set the one- or multi-line format of the print-out, the -normalization of thermodynamic output (total values versus per-atom -values for extensive quantities (ones which scale with the number of -atoms in the system), and the numeric precision of each printed value. -

    -

    IMPORTANT NOTE: When you use a "thermo_style" command, all -thermodynamic settings are restored to their default values, including -those previously set by a thermo_modify command. -Thus if your input script specifies a thermo_style command, you should -use the thermo_modify command after it. -

    -
    - -

    Several of the thermodynamic quantities require a temperature to be -computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc. By -default this is done by using a temperature compute which is created -when LAMMPS starts up, as if this command had been issued: -

    -
    compute thermo_temp all temp 
-
    -

    See the compute temp command for details. Note -that the ID of this compute is thermo_temp and the group is all. -You can change the attributes of this temperature (e.g. its -degrees-of-freedom) via the compute_modify -command. Alternatively, you can directly assign a new compute (that -calculates temperature) which you have defined, to be used for -calculating any thermodynamic quantity that requires a temperature. -This is done via the thermo_modify command. -

    -

    Several of the thermodynamic quantities require a pressure to be -computed: "press", "enthalpy", "pxx", etc. By default this is done by -using a pressure compute which is created when LAMMPS starts up, as -if this command had been issued: -

    -
    compute thermo_press all pressure thermo_temp 
-
    -

    See the compute pressure command for details. -Note that the ID of this compute is thermo_press and the group is -all. You can change the attributes of this pressure via the -compute_modify command. Alternatively, you can -directly assign a new compute (that calculates pressure) which you -have defined, to be used for calculating any thermodynamic quantity -that requires a pressure. This is done via the -thermo_modify command. -

    -

    Several of the thermodynamic quantities require a potential energy to -be computed: "pe", "etotal", "ebond", etc. This is done by using a -pe compute which is created when LAMMPS starts up, as if this -command had been issued: -

    -
    compute thermo_pe all pe 
-
    -

    See the compute pe command for details. Note that -the ID of this compute is thermo_pe and the group is all. You can -change the attributes of this potential energy via the -compute_modify command. -

    -
    - -

    The kinetic energy of the system ke is inferred from the temperature -of the system with 1/2 Kb T of energy for each degree of freedom. -Thus, using different compute commands for calculating -temperature, via the thermo_modify temp command, -may yield different kinetic energies, since different computes that -calculate temperature can subtract out different non-thermal -components of velocity and/or include different degrees of freedom -(translational, rotational, etc). -

    -

    The potential energy of the system pe will include contributions -from fixes if the fix_modify thermo option is set -for a fix that calculates such a contribution. For example, the fix -wall/lj93 fix calculates the energy of atoms -interacting with the wall. See the doc pages for "individual fixes" -to see which ones contribute. -

    -

    A long-range tail correction etail for the VanderWaal pairwise -energy will be non-zero only if the pair_modify -tail option is turned on. The etail contribution -is included in evdwl, pe, and etotal, and the corresponding tail -correction to the pressure is included in press and pxx, pyy, -etc. -

    -
    - -

    The step, elapsed, and elaplong keywords refer to timestep -count. Step is the current timestep, or iteration count when a -minimization is being performed. Elapsed is the -number of timesteps elapsed since the beginning of this run. -Elaplong is the number of timesteps elapsed since the beginning of -an initial run in a series of runs. See the start and stop -keywords for the run for info on how to invoke a series of -runs that keep track of an initial starting time. If these keywords -are not used, then elapsed and elaplong are the same value. -

    -

    The dt keyword is the current timestep size in time -units. The time keyword is the current elapsed -simulation time, also in time units, which is simply -(step*dt) if the timestep size has not changed and the timestep has -not been reset. If the timestep has changed (e.g. via fix -dt/reset) or the timestep has been reset (e.g. via -the "reset_timestep" command), then the simulation time is effectively -a cummulative value up to the current point. -

    -

    The cpu keyword is elapsed CPU seconds since the beginning of this -run. The tpcpu and spcpu keywords are measures of how fast your -simulation is currently running. The tpcpu keyword is simulation -time per CPU second, where simulation time is in time -units. E.g. for metal units, the tpcpu value would be -picoseconds per CPU second. The spcpu keyword is the number of -timesteps per CPU second. Both quantities are on-the-fly metrics, -measured relative to the last time they were invoked. Thus if you are -printing out thermodyamic output every 100 timesteps, the two keywords -will continually output the time and timestep rate for the last 100 -steps. The tpcpu keyword does not attempt to track any changes in -timestep size, e.g. due to using the fix dt/reset -command. -

    -

    The cpuremain keyword estimates the CPU time remaining in the -current run, based on the time elapsed thus far. It will only be a -good estimate if the CPU time/timestep for the rest of the run is -similar to the preceding timesteps. On the initial timestep the value -will be 0.0 since there is no history to estimate from. For a -minimization run performed by the "minimize" command, the estimate is -based on the maxiter parameter, assuming the minimization will -proceed for the maximum number of allowed iterations. -

    -

    The part keyword is useful for multi-replica or multi-partition -simulations to indicate which partition this output and this file -corresponds to, or for use in a variable to append to -a filename for output specific to this partition. See Section_start -7 of the manual for details on running in -multi-partition mode. -

    -

    The fmax and fnorm keywords are useful for monitoring the progress -of an energy minimization. The fmax keyword -calculates the maximum force in any dimension on any atom in the -system, or the infinity-norm of the force vector for the system. The -fnorm keyword calculates the 2-norm or length of the force vector. -

    -

    The nbuild and ndanger keywords are useful for monitoring neighbor -list builds during a run. Note that both these values are also -printed with the end-of-run statistics. The nbuild keyword is the -number of re-builds during the current run. The ndanger keyword is -the number of re-builds that LAMMPS considered potentially -"dangerous". If atom movement triggered neighbor list rebuilding (see -the neigh_modify command), then dangerous -reneighborings are those that were triggered on the first timestep -atom movement was checked for. If this count is non-zero you may wish -to reduce the delay factor to insure no force interactions are missed -by atoms moving beyond the neighbor skin distance before a rebuild -takes place. -

    -

    The keywords cella, cellb, cellc, cellalpha, cellbeta, -cellgamma, correspond to the usual crystallographic quantities that -define the periodic unit cell of a crystal. See this -section of the doc pages for a geometric -description of triclinic periodic cells, including a precise defintion -of these quantities in terms of the internal LAMMPS cell dimensions -lx, ly, lz, yz, xz, xy. -

    -
    - -

    The c_ID and c_ID[I] and c_ID[I][J] keywords allow global -values calculated by a compute to be output. As discussed on the -compute doc page, computes can calculate global, -per-atom, or local values. Only global values can be referenced by -this command. However, per-atom compute values can be referenced in a -variable and the variable referenced by thermo_style -custom, as discussed below. -

    -

    The ID in the keyword should be replaced by the actual ID of a compute -that has been defined elsewhere in the input script. See the -compute command for details. If the compute calculates -a global scalar, vector, or array, then the keyword formats with 0, 1, -or 2 brackets will reference a scalar value from the compute. -

    -

    Note that some computes calculate "intensive" global quantities like -temperature; others calculate "extensive" global quantities like -kinetic energy that are summed over all atoms in the compute group. -Intensive quantities are printed directly without normalization by -thermo_style custom. Extensive quantities may be normalized by the -total number of atoms in the simulation (NOT the number of atoms in -the compute group) when output, depending on the thermo_modify -norm option being used. -

    -

    The f_ID and f_ID[I] and f_ID[I][J] keywords allow global -values calculated by a fix to be output. As discussed on the -fix doc page, fixes can calculate global, per-atom, or -local values. Only global values can be referenced by this command. -However, per-atom fix values can be referenced in a -variable and the variable referenced by thermo_style -custom, as discussed below. -

    -

    The ID in the keyword should be replaced by the actual ID of a fix -that has been defined elsewhere in the input script. See the -fix command for details. If the fix calculates a global -scalar, vector, or array, then the keyword formats with 0, 1, or 2 -brackets will reference a scalar value from the fix. -

    -

    Note that some fixes calculate "intensive" global quantities like -timestep size; others calculate "extensive" global quantities like -energy that are summed over all atoms in the fix group. Intensive -quantities are printed directly without normalization by thermo_style -custom. Extensive quantities may be normalized by the total number of -atoms in the simulation (NOT the number of atoms in the fix group) -when output, depending on the thermo_modify norm -option being used. -

    -

    The v_name keyword allow the current value of a variable to be -output. The name in the keyword should be replaced by the variable -name that has been defined elsewhere in the input script. Only -equal-style variables can be referenced. See the -variable command for details. Variables of style -equal can reference per-atom properties or thermodynamic keywords, -or they can invoke other computes, fixes, or variables when evaluated, -so this is a very general means of creating thermodynamic output. -

    -

    Note that equal-style variables are assumed to be "intensive" global -quantities, which are thus printed as-is, without normalization by -thermo_style custom. You can include a division by "natoms" in the -variable formula if this is not the case. -

    -
    - -

    Restrictions: -

    -

    This command must come after the simulation box is defined by a -read_data, read_restart, or -create_box command. -

    -

    Related commands: -

    -

    thermo, thermo_modify, -fix_modify, compute temp, -compute pressure -

    -

    Default: -

    -
    thermo_style one 
-
    - diff --git a/doc/doc2/timer.html b/doc/doc2/timer.html deleted file mode 100644 index 95cc06f011..0000000000 --- a/doc/doc2/timer.html +++ /dev/null @@ -1,79 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    timer command -

    -

    Syntax: -

    -
    timer args 
-
    -
  • args = one or more of off or loop or normal or full or sync or nosync - -
      off = do not collect or print any timing information
-  loop = collect only the total time for the simulation loop
-  normal = collect timer information broken down by sections (default)
-  full = like normal but also include CPU and thread utilzation 
-  sync = explicitly synchronize MPI tasks between sections
-  nosync = do not synchronize MPI tasks between sections (default) 
-
    -

    Examples: -

    -
    timer full sync
-timer loop 
-
    -

    Description: -

    -

    Select the level of detail LAMMPS performs its CPU timings. -

    -

    During a simulation run LAMMPS collects information about how much -time is spent in different sections of the code and thus can provide -valuable information for determining performance and load imbalance -problems. This can be done at different levels of detail and -accuracy. For more information about the timing output, see this -discussion of screen output. -

    -

    The off setting will turn all time measurements off. The loop -setting will only measure the total time for a run and not collect any -detailed per section information. With the normal setting, timing -information for portions of the timestep (pairwise calculations, -neighbor list construction, output, etc) are collected as well as -information about load imbalances for those sections across -procsessors. The full setting adds information about CPU -utilization and thread utilization, when multi-threading is enabled. -

    -

    With the sync setting, all MPI tasks are synchronized at each timer -call which meaures load imbalance more accuractly, though it can also -slow down the simulation. Using the nosync setting (which is the -default) turns off this synchronization. -

    -

    Multiple keywords can be specified. For keywords that are mutually -exclusive, the last one specified takes effect. -

    -

    IMPORTANT NOTE: Using the full and sync options provides the most -detailed and accurate timing information, but can also have a negative -performance impact due to the overhead of the many required system -calls. It is thus recommended to use these settings only when testing -tests to identify performance bottlenecks. For calculations with few -atoms or a very large number of processors, even the normal setting -can have a measurable negative performance impact. In those cases you -can just use the loop or off setting. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    run post no, kspace_modify fftbench -

    -

    Default: -

    -

    timer normal nosync -

    - diff --git a/doc/doc2/timestep.html b/doc/doc2/timestep.html deleted file mode 100644 index 2d295005c8..0000000000 --- a/doc/doc2/timestep.html +++ /dev/null @@ -1,58 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    timestep command -

    -

    Syntax: -

    -
    timestep dt 
-
    -
    • dt = timestep size (time units) -
    -

    Examples: -

    -
    timestep 2.0 
-timestep 0.003 
-
    -

    Description: -

    -

    Set the timestep size for subsequent molecular dynamics simulations. -See the units command for the time units associated with -each choice of units that LAMMPS supports. -

    -

    The default value for the timestep size also depends on the choice of -units for the simulation; see the default values below. -

    -

    When the run style is respa, dt is the timestep for -the outer loop (largest) timestep. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix dt/reset, run, -run_style respa, units -

    -

    Default: -

    -
    - - - - - - - - -
    choice of units time units default timestep size
    lj tau 0.005 tau
    real fmsec 1.0 fmsec
    metal psec 0.001 psec
    si sec 1.0e-8 sec (10 nsec)
    cgs sec 1.0e-8 sec (10 nsec)
    electron fmsec 0.001 fmsec
    micro usec 2.0 usec
    nano nsec 0.00045 nsec -
    - - diff --git a/doc/doc2/tutorial_drude.html b/doc/doc2/tutorial_drude.html deleted file mode 100644 index b900440292..0000000000 --- a/doc/doc2/tutorial_drude.html +++ /dev/null @@ -1,467 +0,0 @@ - - - - -

    Tutorial for Thermalized Drude oscillators in LAMMPS -

    -

    This tutorial explains how to use Drude oscillators in LAMMPS to -simulate polarizable systems using the USER-DRUDE package. As an -illustration, the input files for a simulation of 250 phenol molecules -are documented. First of all, LAMMPS has to be compiled with the -USER-DRUDE package activated. Then, the data file and input scripts -have to be modified to include the Drude dipoles and how to handle -them. -

    -
    - -

    Overview of Drude induced dipoles -

    -

    Polarizable atoms acquire an induced electric dipole moment under the -action of an external electric field, for example the electric field -created by the surrounding particles. Drude oscillators represent -these dipoles by two fixed charges: the core (DC) and the Drude -particle (DP) bound by a harmonic potential. The Drude particle can be -thought of as the electron cloud whose center can be displaced from -the position of the the corresponding nucleus. -

    -

    The sum of the masses of a core-Drude pair should be the mass of the -initial (unsplit) atom, \(m_C + m_D = m\). The sum of their charges -should be the charge of the initial (unsplit) atom, \(q_C + q_D = q\). -A harmonic potential between the core and Drude partners should be -present, with force constant \(k_D\) and an equilibrium distance of -zero. The (half-)stiffness of the harmonic bond -\(K_D = k_D/2\) and the Drude charge \(q_D\) are related to the atom -polarizability \(\alpha\) by -

    -

    \begin{equation} K_D = \frac 1 2\, \frac {q_D^2} \alpha -\end{equation} -

    -

    Ideally, the mass of the Drude particle should be small, and the -stiffness of the harmonic bond should be large, so that the Drude -particle remains close ot the core. The values of Drude mass, Drude -charge, and force constant can be chosen following different -strategies, as in the following examples of polarizable force -fields. -

    -
    • Lamoureux and Roux suggest adopting a global -half-stiffness, \(K_D\) = 500 kcal/(mol Å2) — -which corresponds to a force constant \(k_D\) = 4184 kJ/(mol -Å2) — for all types of core-Drude bond, a -global mass \(m_D\) = 0.4 g/mol (or u) for all types of Drude -particle, and to calculate the Drude charges for individual atom types -from the atom polarizabilities using equation (1). This choice is -followed in the polarizable CHARMM force field. - -
    • Schroeder and Steinhauser suggest adopting a global -charge \(q_D\) = -1.0e and a global mass \(m_D\) = 0.1 g/mol (or u) -for all Drude particles, and to calculate the force constant for each -type of core-Drude bond from equation (1). The timesteps used by these -authors are between 0.5 and 2 fs, with the degrees of freedom of the -Drude oscillators kept cold at 1 K. In both these force fields -hydrogen atoms are treated as non-polarizable. -
    -

    The motion of of the Drude particles can be calculated by minimizing -the energy of the induced dipoles at each timestep, by an interative, -self-consistent procedure. The Drude particles can be massless and -therefore do not contribute to the kinetic energy. However, the -relaxed method is computationall slow. An extended-lagrangian method -can be used to calculate the positions of the Drude particles, but -this requires them to have mass. It is important in this case to -decouple the degrees of freedom associated with the Drude oscillators -from those of the normal atoms. Thermalizing the Drude dipoles at -temperatures comparable to the rest of the simulation leads to several -problems (kinetic energy transfer, very short timestep, etc.), which -can be remediated by the "cold Drude" technique (Lamoureux and -Roux). -

    -

    Two closely related models are used to represent polarization through -"charges on a spring": the core-shell model and the Drude -model. Although the basic idea is the same, the core-shell model is -normally used for ionic/crystalline materials, whereas the Drude model -is normally used for molecular systems and fluid states. In ionic -crystals the symmetry around each ion and the distance between them -are such that the core-shell model is sufficiently stable. But to be -applicable to molecular/covalent systems the Drude model includes two -important features: -

    -
    1. The possibility to thermostat the additional degrees of freedom -associated with the induced dipoles at very low temperature, in terms -of the reduced coordinates of the Drude particles with respect to -their cores. This makes the trajectory close to that of relaxed -induced dipoles. - -
    2. The Drude dipoles on covalently bonded atoms interact too strongly -due to the short distances, so an atom may capture the Drude particle -(shell) of a neighbor, or the induced dipoles within the same molecule -may align too much. To avoid this, damping at short of the -interactions between the point charges composing the induced dipole -can be done by Thole functions. -
    -
    - -

    Preparation of the data file -

    -

    The data file is similar to a standard LAMMPS data file for -atom_style full. The DPs and the harmonic bonds connecting them -to their DC should appear in the data file as normal atoms and bonds. -

    -

    You can use the polarizer tool (Python script distributed with the -USER-DRUDE package) to convert a non-polarizable data file (here -data.102494.lmp) to a polarizable data file (data-p.lmp) -

    -
    polarizer -q -f phenol.dff data.102494.lmp data-p.lmp 
-
    -

    This will automatically insert the new atoms and bonds. -The masses and charges of DCs and DPs are computed -from phenol.dff, as well as the DC-DP bond constants. The file -phenol.dff contains the polarizabilities of the atom types -and the mass of the Drude particles, for instance: -

    -
    # units: kJ/mol, A, deg
-# kforce is in the form k/2 r_D^2
-# type  m_D/u   q_D/e    k_D   alpha/A3  thole
-OH      0.4    -1.0    4184.0   0.63     0.67
-CA      0.4    -1.0    4184.0   1.36     2.51
-CAI     0.4    -1.0    4184.0   1.09     2.51 
-
    -

    The hydrogen atoms are absent from this file, so they will be treated -as non-polarizable atoms. In the non-polarizable data file -data.102494.lmp, atom names corresponding to the atom type numbers -have to be specified as comments at the end of lines of the Masses -section. You probably need to edit it to add these names. It should -look like -

    -
    Masses 
-
    -
    1 12.011 # CAI
-2 12.011 # CA
-3 15.999 # OH
-4 1.008  # HA
-5 1.008  # HO 
-
    -
    - -

    Basic input file -

    -

    The atom style should be set to (or derive from) full, so that you -can define atomic charges and molecular bonds, angles, dihedrals... -

    -

    The polarizer tool also outputs certain lines related to the input -script (the use of these lines will be explained below). In order for -LAMMPS to recognize that you are using Drude oscillators, you should -use the fix drude. The command is -

    -
    fix DRUDE all drude C C C N N D D D 
-
    -

    The N, C, D following the drude keyword have the following meaning: -There is one tag for each atom type. This tag is C for DCs, D for DPs -and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O -atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and -the atom types 6 to 8 are the newly created DPs. -

    -

    By recognizing the fix drude, LAMMPS will find and store matching -DC-DP pairs and will treat DP as equivalent to their DC in the -special bonds relations. It may be necessary to extend the space -for storing such special relations. In this case extra space should -be reserved by using the extra keyword of the special_bonds -command. With our phenol, there is 1 more special neighbor for which -space is required. Otherwise LAMMPS crashes and gives the required -value. -

    -
    special_bonds lj/coul 0.0 0.0 0.5 extra 1 
-
    -

    Let us assume we want to run a simple NVT simulation at 300 K. Note -that Drude oscillators need to be thermalized at a low temperature in -order to approximate a self-consistent field (SCF), therefore it is not -possible to simulate an NVE ensemble with this package. Since dipoles -are approximated by a charged DC-DP pair, the pair_style must -include Coulomb interactions, for instance lj/cut/coul/long with -kspace_style pppm. For example, with a cutoff of 10. and a precision -1.e-4: -

    -
    pair_style lj/cut/coul/long 10.0
-kspace_style pppm 1.0e-4 
-
    -

    As compared to the non-polarizable input file, pair_coeff lines need -to be added for the DPs. Since the DPs have no Lennard-Jones -interactions, their epsilon is 0. so the only pair_coeff line -that needs to be added is -

    -
    pair_coeff * 6* 0.0 0.0 # All-DPs 
-
    -

    Now for the thermalization, the simplest choice is to use the fix -langevin/drude. -

    -
    fix LANG all langevin/drude 300. 100 12435 1. 20 13977 
-
    -

    This applies a Langevin thermostat at temperature 300. to the centers -of mass of the DC-DP pairs, with relaxation time 100 and with random -seed 12345. This fix applies also a Langevin thermostat at temperature -1. to the relative motion of the DPs around their DCs, with relaxation -time 20 and random seed 13977. Only the DCs and non-polarizable -atoms need to be in this fix's group. LAMMPS will thermostate the DPs -together with their DC. For this, ghost atoms need to know their -velocities. Thus you need to add the following command: -

    -
    comm_modify vel yes 
-
    -

    In order to avoid that the center of mass of the whole system -drifts due to the random forces of the Langevin thermostat on DCs, you -can add the zero yes option at the end of the fix line. -

    -

    If the fix shake is used to constrain the C-H bonds, it should be -invoked after the fix langevin/drude for more accuracy. -

    -
    fix SHAKE ATOMS shake 0.0001 20 0 t 4 5 
-
    -

    IMPORTANT NOTE: The group of the fix shake must not include the DPs. -If the group ATOMS is defined by non-DPs atom types, you could use -

    -

    Since the fix langevin/drude does not perform time integration (just -modification of forces but no position/velocity updates), the fix -nve should be used in conjunction. -

    -
    fix NVE all nve 
-
    -

    Finally, do not forget to update the atom type elements if you use -them in a dump_modify ... element ... command, by adding the element -type of the DPs. Here for instance -

    -
    dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify DUMP element C C O H H D D D 
-
    -

    The input file should now be ready for use! -

    -

    You will notice that the global temperature thermo_temp computed by -LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as -standard atoms in his default compute. If you want to output the -temperatures of the DC-DP pair centers of mass and of the DPs relative -to their DCs, you should use the compute -temp_drude -

    -
    compute TDRUDE all temp/drude 
-
    -

    And then output the correct temperatures of the Drude oscillators -using thermo_style custom with respectively c_TDRUDE[1] and -c_TDRUDE[2]. These should be close to 300.0 and 1.0 on average. -

    -
    thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2] 
-
    -
    - -

    Thole screening -

    -

    Dipolar interactions represented by point charges on springs may not -be stable, for example if the atomic polarizability is too high for -instance, a DP can escape from its DC and be captured by another DC, -which makes the force and energy diverge and the simulation -crash. Even without reaching this extreme case, the correlation -between nearby dipoles on the same molecule may be exagerated. Often, -special bond relations prevent bonded neighboring atoms to see the -charge of each other's DP, so that the problem does not always appear. -It is possible to use screened dipole dipole interactions by using the -pair_style thole. This is implemented as a -correction to the Coulomb pair_styles, which dampens at short distance -the interactions between the charges representing the induced dipoles. -It is to be used as hybrid/overlay with any standard coul pair -style. In our example, we would use -

    -
    pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0 
-
    -

    This tells LAMMPS that we are using two pair_styles. The first one is -as above (lj/cut/coul/long 10.0). The second one is a thole -pair_style with default screening factor 2.6 (Noskov) and -cutoff 10.0. -

    -

    Since hybrid/overlay does not support mixing rules, the interaction -coefficients of all the pairs of atom types with i < j should be -explicitly defined. The output of the polarizer script can be used -to complete the pair_coeff section of the input file. In our -example, this will look like: -

    -
    pair_coeff    1    1 lj/cut/coul/long    0.0700   3.550
-pair_coeff    1    2 lj/cut/coul/long    0.0700   3.550
-pair_coeff    1    3 lj/cut/coul/long    0.1091   3.310
-pair_coeff    1    4 lj/cut/coul/long    0.0458   2.985
-pair_coeff    2    2 lj/cut/coul/long    0.0700   3.550
-pair_coeff    2    3 lj/cut/coul/long    0.1091   3.310
-pair_coeff    2    4 lj/cut/coul/long    0.0458   2.985
-pair_coeff    3    3 lj/cut/coul/long    0.1700   3.070
-pair_coeff    3    4 lj/cut/coul/long    0.0714   2.745
-pair_coeff    4    4 lj/cut/coul/long    0.0300   2.420
-pair_coeff    *    5 lj/cut/coul/long    0.0000   0.000
-pair_coeff    *   6* lj/cut/coul/long    0.0000   0.000
-pair_coeff    1    1 thole   1.090   2.510
-pair_coeff    1    2 thole   1.218   2.510
-pair_coeff    1    3 thole   0.829   1.590
-pair_coeff    1    6 thole   1.090   2.510
-pair_coeff    1    7 thole   1.218   2.510
-pair_coeff    1    8 thole   0.829   1.590
-pair_coeff    2    2 thole   1.360   2.510
-pair_coeff    2    3 thole   0.926   1.590
-pair_coeff    2    6 thole   1.218   2.510
-pair_coeff    2    7 thole   1.360   2.510
-pair_coeff    2    8 thole   0.926   1.590
-pair_coeff    3    3 thole   0.630   0.670
-pair_coeff    3    6 thole   0.829   1.590
-pair_coeff    3    7 thole   0.926   1.590
-pair_coeff    3    8 thole   0.630   0.670
-pair_coeff    6    6 thole   1.090   2.510
-pair_coeff    6    7 thole   1.218   2.510
-pair_coeff    6    8 thole   0.829   1.590
-pair_coeff    7    7 thole   1.360   2.510
-pair_coeff    7    8 thole   0.926   1.590
-pair_coeff    8    8 thole   0.630   0.670 
-
    -

    For the thole pair style the coefficients are -

    -
    1. the atom polarizability in units of cubic length - -
    2. the screening factor of the Thole function (optional, default value -specified by the pair_style command) - -
    3. the cutoff (optional, default value defined by the pair_style command) - -
    -

    The special neighbors have charge-charge and charge-dipole -interactions screened by the coul factors of the special_bonds -command (0.0, 0.0, and 0.5 in the example above). Without using the -pair_style thole, dipole-dipole interactions are screened by the -same factor. By using the pair_style thole, dipole-dipole -interactions are screened by Thole's function, whatever their special -relationship (except within each DC-DP pair of course). Consider for -example 1-2 neighbors: using the pair_style thole, their dipoles -will see each other (despite the coul factor being 0.) and the -interactions between these dipoles will be damped by Thole's function. -

    -
    - -

    Thermostats and barostats -

    -

    Using a Nose-Hoover barostat with the langevin/drude thermostat is -straightforward using fix nph instead of nve. For example: -

    -
    fix NPH all nph iso 1. 1. 500 
-
    -

    It is also possible to use a Nose-Hoover instead of a Langevin -thermostat. This requires to use fix -drude/transform just before and after the -time intergation fixes. The fix drude/transform/direct converts the -atomic masses, positions, velocities and forces into a reduced -representation, where the DCs transform into the centers of mass of -the DC-DP pairs and the DPs transform into their relative position -with respect to their DC. The fix drude/transform/inverse performs -the reverse transformation. For a NVT simulation, with the DCs and -atoms at 300 K and the DPs at 1 K relative to their DC one would use -

    -
    fix DIRECT all drude/transform/direct
-fix NVT1 ATOMS nvt temp 300. 300. 100
-fix NVT2 DRUDES nvt temp 1. 1. 20
-fix INVERSE all drude/transform/inverse 
-
    -

    For our phenol example, the groups would be defined as -

    -
    group ATOMS  type 1 2 3 4 5 # DCs and non-polarizable atoms
-group CORES  type 1 2 3     # DCs
-group DRUDES type 6 7 8     # DPs 
-
    -

    Note that with the fixes drude/transform, it is not required to -specify comm_modify vel yes because the fixes do it anyway (several -times and for the forces also). To avoid the flying ice cube artifact -(Lamoureux), where the atoms progressively freeze and the -center of mass of the whole system drifts faster and faster, the fix -momentum can be used. For instance: -

    -
    fix MOMENTUM all momentum 100 linear 1 1 1 
-
    -

    It is a bit more tricky to run a NPT simulation with Nose-Hoover -barostat and thermostat. First, the volume should be integrated only -once. So the fix for DCs and atoms should be npt while the fix for -DPs should be nvt (or vice versa). Second, the fix npt computes a -global pressure and thus a global temperature whatever the fix group. -We do want the pressure to correspond to the whole system, but we want -the temperature to correspond to the fix group only. We must then use -the fix_modify command for this. In the end, the block of -instructions for thermostating and barostating will look like -

    -
    compute TATOMS ATOMS temp
-fix DIRECT all drude/transform/direct
-fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500
-fix_modify NPT temp TATOMS press thermo_press
-fix NVT DRUDES nvt temp 1. 1. 20
-fix INVERSE all drude/transform/inverse 
-
    -
    - -

    Rigid bodies -

    -

    You may want to simulate molecules as rigid bodies (but polarizable). -Common cases are water models such as SWM4-NDP, which is a -kind of polarizable TIP4P water. The rigid bodies and the DPs should -be integrated separately, even with the Langevin thermostat. Let us -review the different thermostats and ensemble combinations. -

    -

    NVT ensemble using Langevin thermostat: -

    -
    comm_modify vel yes
-fix LANG all langevin/drude 300. 100 12435 1. 20 13977
-fix RIGID ATOMS rigid/nve/small molecule
-fix NVE DRUDES nve 
-
    -

    NVT ensemble using Nose-Hoover thermostat: -

    -
    fix DIRECT all drude/transform/direct
-fix RIGID ATOMS rigid/nvt/small molecule temp 300. 300. 100
-fix NVT DRUDES nvt temp 1. 1. 20
-fix INVERSE all drude/transform/inverse 
-
    -

    NPT ensemble with Langevin thermostat: -

    -
    comm_modify vel yes
-fix LANG all langevin/drude 300. 100 12435 1. 20 13977
-fix RIGID ATOMS rigid/nph/small molecule iso 1. 1. 500
-fix NVE DRUDES nve 
-
    -

    NPT ensemble using Nose-Hoover thermostat: -

    -
    compute TATOM ATOMS temp
-fix DIRECT all drude/transform/direct
-fix RIGID ATOMS rigid/npt/small molecule temp 300. 300. 100 iso 1. 1. 500
-fix_modify RIGID temp TATOM press thermo_press
-fix NVT DRUDES nvt temp 1. 1. 20
-fix INVERSE all drude/transform/inverse 
-
    -
    - - - -

    (Lamoureux) Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) -

    - - -

    (Schroeder) Schröder and Steinhauser, J Chem Phys, 133, -154511 (2010). -

    - - -

    (Jiang) Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, - J Phys Chem Lett, 2, 87-92 (2011). -

    - - -

    (Thole) Chem Phys, 59, 341 (1981). -

    - - -

    (Noskov) Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). -

    - - -

    (SWM4-NDP) Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys -Let, 418, 245-249 (2006) -

    - diff --git a/doc/doc2/uncompute.html b/doc/doc2/uncompute.html deleted file mode 100644 index 8487f4aac6..0000000000 --- a/doc/doc2/uncompute.html +++ /dev/null @@ -1,39 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    uncompute command -

    -

    Syntax: -

    -
    uncompute compute-ID 
-
    -
    • compute-ID = ID of a previously defined compute -
    -

    Examples: -

    -
    uncompute 2
-uncompute lower-boundary 
-
    -

    Description: -

    -

    Delete a compute that was previously defined with a compute -command. This also wipes out any additional changes made to the compute -via the compute_modify command. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    compute -

    -

    Default: none -

    - diff --git a/doc/doc2/undump.html b/doc/doc2/undump.html deleted file mode 100644 index 246fe03756..0000000000 --- a/doc/doc2/undump.html +++ /dev/null @@ -1,38 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    undump command -

    -

    Syntax: -

    -
    undump dump-ID 
-
    -
    • dump-ID = ID of previously defined dump -
    -

    Examples: -

    -
    undump mine
-undump 2 
-
    -

    Description: -

    -

    Turn off a previously defined dump so that it is no longer active. -This closes the file associated with the dump. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    dump -

    -

    Default: none -

    - diff --git a/doc/doc2/unfix.html b/doc/doc2/unfix.html deleted file mode 100644 index 2ae948c2c8..0000000000 --- a/doc/doc2/unfix.html +++ /dev/null @@ -1,39 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    unfix command -

    -

    Syntax: -

    -
    unfix fix-ID 
-
    -
    • fix-ID = ID of a previously defined fix -
    -

    Examples: -

    -
    unfix 2
-unfix lower-boundary 
-
    -

    Description: -

    -

    Delete a fix that was previously defined with a fix -command. This also wipes out any additional changes made to the fix -via the fix_modify command. -

    -

    Restrictions: none -

    -

    Related commands: -

    -

    fix -

    -

    Default: none -

    - diff --git a/doc/doc2/units.html b/doc/doc2/units.html deleted file mode 100644 index d532b2ae32..0000000000 --- a/doc/doc2/units.html +++ /dev/null @@ -1,223 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    units command -

    -

    Syntax: -

    -
    units style 
-
    -
    • style = lj or real or metal or si or cgs or electron or micro or nano -
    -

    Examples: -

    -
    units metal
-units lj 
-
    -

    Description: -

    -

    This command sets the style of units used for a simulation. It -determines the units of all quantities specified in the input script -and data file, as well as quantities output to the screen, log file, -and dump files. Typically, this command is used at the very beginning -of an input script. -

    -

    For all units except lj, LAMMPS uses physical constants from -www.physics.nist.gov. For the definition of Kcal in real units, -LAMMPS uses the thermochemical calorie = 4.184 J. -

    -

    The choice you make for units simply sets some internal conversion -factors within LAMMPS. This means that any simulation you perform for -one choice of units can be duplicated with any other unit setting -LAMMPS supports. In this context "duplicate" means the particles will -have identical trajectories and all output generated by the simulation -will be identical. This will be the case for some number of timesteps -until round-off effects accumulate, since the conversion factors for -two different unit systems are not identical to infinite precision. -

    -

    To perform the same simulation in a different set of units you must -change all the unit-based input parameters in your input script and -other input files (data file, potential files, etc) correctly to the -new units. And you must correctly convert all output from the new -units to the old units when comparing to the original results. That -is often not simple to do. -

    -
    - -

    For style lj, all quantities are unitless. Without loss of -generality, LAMMPS sets the fundamental quantities mass, sigma, -epsilon, and the Boltzmann constant = 1. The masses, distances, -energies you specify are multiples of these fundamental values. The -formulas relating the reduced or unitless quantity (with an asterisk) -to the same quantity with units is also given. Thus you can use the -mass & sigma & epsilon values for a specific material and convert the -results from a unitless LJ simulation into physical quantities. -

    -
    • mass = mass or m -
    • distance = sigma, where x* = x / sigma -
    • time = tau, where t* = t (epsilon / m / sigma^2)^1/2 -
    • energy = epsilon, where E* = E / epsilon -
    • velocity = sigma/tau, where v* = v tau / sigma -
    • force = epsilon/sigma, where f* = f sigma / epsilon -
    • torque = epsilon, where t* = t / epsilon -
    • temperature = reduced LJ temperature, where T* = T Kb / epsilon -
    • pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon -
    • dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau -
    • charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2 -
    • dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2 -
    • electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon -
    • density = mass/volume, where rho* = rho sigma^dim -
    -

    Note that for LJ units, the default mode of thermodyamic output via -the thermo_style command is to normalize energies -by the number of atoms, i.e. energy/atom. This can be changed via the -thermo_modify norm command. -

    -

    For style real, these are the units: -

    -
    • mass = grams/mole -
    • distance = Angstroms -
    • time = femtoseconds -
    • energy = Kcal/mole -
    • velocity = Angstroms/femtosecond -
    • force = Kcal/mole-Angstrom -
    • torque = Kcal/mole -
    • temperature = Kelvin -
    • pressure = atmospheres -
    • dynamic viscosity = Poise -
    • charge = multiple of electron charge (1.0 is a proton) -
    • dipole = charge*Angstroms -
    • electric field = volts/Angstrom -
    • density = gram/cm^dim -
    -

    For style metal, these are the units: -

    -
    • mass = grams/mole -
    • distance = Angstroms -
    • time = picoseconds -
    • energy = eV -
    • velocity = Angstroms/picosecond -
    • force = eV/Angstrom -
    • torque = eV -
    • temperature = Kelvin -
    • pressure = bars -
    • dynamic viscosity = Poise -
    • charge = multiple of electron charge (1.0 is a proton) -
    • dipole = charge*Angstroms -
    • electric field = volts/Angstrom -
    • density = gram/cm^dim -
    -

    For style si, these are the units: -

    -
    • mass = kilograms -
    • distance = meters -
    • time = seconds -
    • energy = Joules -
    • velocity = meters/second -
    • force = Newtons -
    • torque = Newton-meters -
    • temperature = Kelvin -
    • pressure = Pascals -
    • dynamic viscosity = Pascal*second -
    • charge = Coulombs (1.6021765e-19 is a proton) -
    • dipole = Coulombs*meters -
    • electric field = volts/meter -
    • density = kilograms/meter^dim -
    -

    For style cgs, these are the units: -

    -
    • mass = grams -
    • distance = centimeters -
    • time = seconds -
    • energy = ergs -
    • velocity = centimeters/second -
    • force = dynes -
    • torque = dyne-centimeters -
    • temperature = Kelvin -
    • pressure = dyne/cm^2 or barye = 1.0e-6 bars -
    • dynamic viscosity = Poise -
    • charge = statcoulombs or esu (4.8032044e-10 is a proton) -
    • dipole = statcoul-cm = 10^18 debye -
    • electric field = statvolt/cm or dyne/esu -
    • density = grams/cm^dim -
    -

    For style electron, these are the units: -

    -
    • mass = atomic mass units -
    • distance = Bohr -
    • time = femtoseconds -
    • energy = Hartrees -
    • velocity = Bohr/atomic time units [1.03275e-15 seconds] -
    • force = Hartrees/Bohr -
    • temperature = Kelvin -
    • pressure = Pascals -
    • charge = multiple of electron charge (1.0 is a proton) -
    • dipole moment = Debye -
    • electric field = volts/cm -
    -

    For style micro, these are the units: -

    -
    • mass = picograms -
    • distance = micrometers -
    • time = microseconds -
    • energy = picogram-micrometer^2/microsecond^2 -
    • velocity = micrometers/microsecond -
    • force = picogram-micrometer/microsecond^2 -
    • torque = picogram-micrometer^2/microsecond^2 -
    • temperature = Kelvin -
    • pressure = picogram/(micrometer-microsecond^2) -
    • dynamic viscosity = picogram/(micrometer-microsecond) -
    • charge = picocoulombs (1.6021765e-7 is a proton) -
    • dipole = picocoulomb-micrometer -
    • electric field = volt/micrometer -
    • density = picograms/micrometer^dim -
    -

    For style nano, these are the units: -

    -
    • mass = attograms -
    • distance = nanometers -
    • time = nanoseconds -
    • energy = attogram-nanometer^2/nanosecond^2 -
    • velocity = nanometers/nanosecond -
    • force = attogram-nanometer/nanosecond^2 -
    • torque = attogram-nanometer^2/nanosecond^2 -
    • temperature = Kelvin -
    • pressure = attogram/(nanometer-nanosecond^2) -
    • dynamic viscosity = attogram/(nanometer-nanosecond) -
    • charge = multiple of electron charge (1.0 is a proton) -
    • dipole = charge-nanometer -
    • electric field = volt/nanometer -
    • density = attograms/nanometer^dim -
    -

    The units command also sets the timestep size and neighbor skin -distance to default values for each style: -

    -
    • For style lj these are dt = 0.005 tau and skin = 0.3 sigma. -
    • For style real these are dt = 1.0 fmsec and skin = 2.0 Angstroms. -
    • For style metal these are dt = 0.001 psec and skin = 2.0 Angstroms. -
    • For style si these are dt = 1.0e-8 sec and skin = 0.001 meters. -
    • For style cgs these are dt = 1.0e-8 sec and skin = 0.1 cm. -
    • For style electron these are dt = 0.001 fmsec and skin = 2.0 Bohr. -
    • For style micro these are dt = 2.0 microsec and skin = 0.1 micrometers. -
    • For style nano these are dt = 0.00045 nanosec and skin = 0.1 nanometers. -
    -

    Restrictions: -

    -

    This command cannot be used after the simulation box is defined by a -read_data or create_box command. -

    -

    Related commands: none -

    -

    Default: -

    -
    units lj 
-
    - diff --git a/doc/doc2/variable.html b/doc/doc2/variable.html deleted file mode 100644 index 104d57dee4..0000000000 --- a/doc/doc2/variable.html +++ /dev/null @@ -1,1218 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    variable command -

    -

    Syntax: -

    -
    variable name style args ... 
-
    -
    • name = name of variable to define - -
    • style = delete or index or loop or world or universe or -uloop or string or format or getenv or file or atomfile or python or equal or atom - -
        delete = no args
-  index args = one or more strings
-  loop args = N
-    N = integer size of loop, loop from 1 to N inclusive
-  loop args = N pad
-    N = integer size of loop, loop from 1 to N inclusive
-    pad = all values will be same length, e.g. 001, 002, ..., 100
-  loop args = N1 N2
-    N1,N2 = loop from N1 to N2 inclusive
-  loop args = N1 N2 pad
-    N1,N2 = loop from N1 to N2 inclusive
-    pad = all values will be same length, e.g. 050, 051, ..., 100
-  world args = one string for each partition of processors
-  universe args = one or more strings
-  uloop args = N
-    N = integer size of loop
-  uloop args = N pad
-    N = integer size of loop
-    pad = all values will be same length, e.g. 001, 002, ..., 100
-  string arg = one string
-  format args = vname fstr
-    vname = name of equal-style variable to evaluate
-    fstr = C-style format string
-  getenv arg = one string
-  file arg = filename
-  atomfile arg = filename
-  python arg = function
-  equal or atom args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
-    numbers = 0.0, 100, -5.4, 2.8e-4, etc
-    constants = PI, version, on, off, true, false, yes, no
-    thermo keywords = vol, ke, press, etc from thermo_style
-    math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
-                     x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x
-    math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
-                     sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
-                     random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
-                     ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), 
-		     stride(x,y,z), stride2(x,y,z,a,b,c), 
-		     vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
-    group functions = count(group), mass(group), charge(group),
-		      xcm(group,dim), vcm(group,dim), fcm(group,dim),
-		      bound(group,dir), gyration(group), ke(group),
-		      angmom(group,dim), torque(group,dim),
-                      inertia(group,dimdim), omega(group,dim)
-    region functions = count(group,region), mass(group,region), charge(group,region),
-		      xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
-		      bound(group,dir,region), gyration(group,region), ke(group,reigon),
-		      angmom(group,dim,region), torque(group,dim,region), 
-		      inertia(group,dimdim,region), omega(group,dim,region)
-    special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
-    feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
-    atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
-    atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
-    compute references = c_ID, c_ID[i], c_ID[i][j]
-    fix references = f_ID, f_ID[i], f_ID[i][j]
-    variable references = v_name, v_name[i] 
-
      - -
    -

    Examples: -

    -
    variable x index run1 run2 run3 run4 run5 run6 run7 run8
-variable LoopVar loop $n
-variable beta equal temp/3.0
-variable b1 equal x[234]+0.5*vol
-variable b1 equal "x[234] + 0.5*vol"
-variable b equal xcm(mol1,x)/2.0
-variable b equal c_myTemp
-variable b atom x*y/vol
-variable foo string myfile
-variable myPy python increase
-variable f file values.txt
-variable temp world 300.0 310.0 320.0 ${Tfinal}
-variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
-variable x uloop 15 pad
-variable str format x %.6g
-variable x delete 
-
    -

    Description: -

    -

    This command assigns one or more strings to a variable name for -evaluation later in the input script or during a simulation. -

    -

    Variables can thus be useful in several contexts. A variable can be -defined and then referenced elsewhere in an input script to become -part of a new input command. For variable styles that store multiple -strings, the next command can be used to increment which -string is assigned to the variable. Variables of style equal store -a formula which when evaluated produces a single numeric value which -can be output either directly (see the print, fix -print, and run every commands) or as part -of thermodynamic output (see the thermo_style -command), or used as input to an averaging fix (see the fix -ave/time command). Variables of style atom store -a formula which when evaluated produces one numeric value per atom -which can be output to a dump file (see the dump custom -command) or used as input to an averaging fix (see the fix -ave/spatial and fix ave/atom -commands). Variables of style atomfile can be used anywhere in an -input script that atom-style variables are used; they get their -per-atom values from a file rather than from a formula. Variables can -be hooked to Python functions using code you provide, so that the -variable gets its value from the evaluation of the Python code. -

    -

    IMPORTANT NOTE: As discussed in Section 3.2 -of the manual, an input script can use "immediate" variables, specified -as $(formula) with parenthesis, where the formula has the same syntax -as equal-style variables described on this page. This is a convenient -way to evaluate a formula immediately without using the variable command -to define a named variable and then evaluate that variable. See below -for a more detailed discussion of this feature. -

    -

    In the discussion that follows, the "name" of the variable is the -arbitrary string that is the 1st argument in the variable command. -This name can only contain alphanumeric characters and underscores. -The "string" is one or more of the subsequent arguments. The "string" -can be simple text as in the 1st example above, it can contain other -variables as in the 2nd example, or it can be a formula as in the 3rd -example. The "value" is the numeric quantity resulting from -evaluation of the string. Note that the same string can generate -different values when it is evaluated at different times during a -simulation. -

    -

    IMPORTANT NOTE: When the input script line is encountered that defines -a variable of style equal or atom or python that contains a -formula or Python code, the formula is NOT immediately evaluated. -It will be evaluated every time when the variable is used instead. -If you simply want to evaluate a formula in place you can use as -so-called. See the section below about "Immediate Evaluation -of Variables" for more details on the topic. This is also true of -a format style variable since it evaluates another variable when -it is invoked. -

    -

    IMPORTANT NOTE: Variables of style equal and atom can be used as -inputs to various other LAMMPS commands which evaluate their formulas -as needed, e.g. at different timesteps during a run. -Variables of style python can be used in place of an equal-style -variable so long as the associated Python function, as defined by the -python command, returns a numeric value. Thus any -command that states it can use an equal-style variable as an argument, -can also use such a python-style variable. This means that when the -LAMMPS command evaluates the variable, the Python function will be -executed. -

    -

    IMPORTANT NOTE: When a variable command is encountered in the input -script and the variable name has already been specified, the command -is ignored. This means variables can NOT be re-defined in an input -script (with two exceptions, read further). This is to allow an input -script to be processed multiple times without resetting the variables; -see the jump or include commands. It also -means that using the command-line switch --var will override a corresponding index variable setting in the input -script. -

    -

    There are two exceptions to this rule. First, variables of style -string, getenv, equal, atom, and python ARE redefined each -time the command is encountered. This allows these style of variables -to be redefined multiple times in an input script. In a loop, this -means the formula associated with an equal or atom style variable -can change if it contains a substitution for another variable, e.g. $x -or v_x. -

    -

    Second, as described below, if a variable is iterated on to the end of -its list of strings via the next command, it is removed -from the list of active variables, and is thus available to be -re-defined in a subsequent variable command. The delete style does -the same thing. -

    -
    - -

    This section of the manual explains how -occurrences of a variable name in an input script line are replaced by -the variable's string. The variable name can be referenced as $x if -the name "x" is a single character, or as ${LoopVar} if the name -"LoopVar" is one or more characters. -

    -

    As described below, for variable styles index, loop, file, -universe, and uloop, which string is assigned to a variable can be -incremented via the next command. When there are no more -strings to assign, the variable is exhausted and a flag is set that -causes the next jump command encountered in the input -script to be skipped. This enables the construction of simple loops -in the input script that are iterated over and then exited from. -

    -

    As explained above, an exhausted variable can be re-used in an input -script. The delete style also removes the variable, the same as if -it were exhausted, allowing it to be redefined later in the input -script or when the input script is looped over. This can be useful -when breaking out of a loop via the if and jump -commands before the variable would become exhausted. For example, -

    -
    label	    loop
-variable    a loop 5
-print	    "A = $a"
-if	    "$a > 2" then "jump in.script break"
-next	    a
-jump	    in.script loop
-label	    break
-variable    a delete 
-
    -
    - -

    This section describes how all the various variable styles are defined -and what they store. Except for the equal and atom styles, -which are explaine in the next section. -

    -

    Many of the styles store one or more strings. Note that a single -string can contain spaces (multiple words), if it is enclosed in -quotes in the variable command. When the variable is substituted for -in another input script command, its returned string will then be -interpreted as multiple arguments in the expanded command. -

    -

    For the index style, one or more strings are specified. Initially, -the 1st string is assigned to the variable. Each time a -next command is used with the variable name, the next -string is assigned. All processors assign the same string to the -variable. -

    -

    Index style variables with a single string value can also be set by -using the command-line switch -var; see this -section for details. -

    -

    The loop style is identical to the index style except that the -strings are the integers from 1 to N inclusive, if only one argument N -is specified. This allows generation of a long list of runs -(e.g. 1000) without having to list N strings in the input script. -Initially, the string "1" is assigned to the variable. Each time a -next command is used with the variable name, the next -string ("2", "3", etc) is assigned. All processors assign the same -string to the variable. The loop style can also be specified with -two arguments N1 and N2. In this case the loop runs from N1 to N2 -inclusive, and the string N1 is initially assigned to the variable. -N1 <= N2 and N2 >= 0 is required. -

    -

    For the world style, one or more strings are specified. There must -be one string for each processor partition or "world". See this -section of the manual for information on -running LAMMPS with multiple partitions via the "-partition" -command-line switch. This variable command assigns one string to each -world. All processors in the world are assigned the same string. The -next command cannot be used with equal style variables, since there -is only one value per world. This style of variable is useful when -you wish to run different simulations on different partitions, or when -performing a parallel tempering simulation (see the -temper command), to assign different temperatures to -different partitions. -

    -

    For the universe style, one or more strings are specified. There -must be at least as many strings as there are processor partitions or -"worlds". See this page for information -on running LAMMPS with multiple partitions via the "-partition" -command-line switch. This variable command initially assigns one -string to each world. When a next command is encountered -using this variable, the first processor partition to encounter it, is -assigned the next available string. This continues until all the -variable strings are consumed. Thus, this command can be used to run -50 simulations on 8 processor partitions. The simulations will be run -one after the other on whatever partition becomes available, until -they are all finished. Universe style variables are incremented -using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock" -which you will see in your directory during such a LAMMPS run. -

    -

    The uloop style is identical to the universe style except that the -strings are the integers from 1 to N. This allows generation of long -list of runs (e.g. 1000) without having to list N strings in the input -script. -

    -

    For the string style, a single string is assigned to the variable. -The only difference between this and using the index style with a -single string is that a variable with string style can be redefined. -E.g. by another command later in the input script, or if the script is -read again in a loop. -

    -

    For the format style, an equal-style variable is specified along -with a C-style format string, e.g. "%f" or "%.10g", which must be -appropriate for formatting a double-precision floating-point value. -This allows an equal-style variable to be formatted specifically for -output as a string, e.g. by the print command, if the -default format "%.15g" has too much precision. -

    -

    For the getenv style, a single string is assigned to the variable -which should be the name of an environment variable. When the -variable is evaluated, it returns the value of the environment -variable, or an empty string if it not defined. This style of -variable can be used to adapt the behavior of LAMMPS input scripts via -environment variable settings, or to retrieve information that has -been previously stored with the shell putenv command. -Note that because environment variable settings are stored by the -operating systems, they persist beyond a clear command. -

    -

    For the file style, a filename is provided which contains a list of -strings to assign to the variable, one per line. The strings can be -numeric values if desired. See the discussion of the next() function -below for equal-style variables, which will convert the string of a -file-style variable into a numeric value in a formula. -

    -

    When a file-style variable is defined, the file is opened and the -string on the first line is read and stored with the variable. This -means the variable can then be evaluated as many times as desired and -will return that string. There are two ways to cause the next string -from the file to be read: use the next command or the -next() function in an equal- or atom-style variable, as discussed -below. -

    -

    The rules for formatting the file are as follows. A comment character -"#" can be used anywhere on a line; text starting with the comment -character is stripped. Blank lines are skipped. The first "word" of -a non-blank line, delimited by white space, is the "string" assigned -to the variable. -

    -

    For the atomfile style, a filename is provided which contains one or -more sets of values, to assign on a per-atom basis to the variable. -The format of the file is described below. -

    -

    When an atomfile-style variable is defined, the file is opened and the -first set of per-atom values are read and stored with the variable. -This means the variable can then be evaluated as many times as desired -and will return those values. There are two ways to cause the next -set of per-atom values from the file to be read: use the -next command or the next() function in an atom-style -variable, as discussed below. -

    -

    The rules for formatting the file are as follows. Each time a set of -per-atom values is read, a non-blank line is searched for in the file. -A comment character "#" can be used anywhere on a line; text starting -with the comment character is stripped. Blank lines are skipped. The -first "word" of a non-blank line, delimited by white space, is read as -the count N of per-atom lines to immediately follow. N can be be the -total number of atoms in the system, or only a subset. The next N -lines have the following format -

    -
    ID value 
-
    -

    where ID is an atom ID and value is the per-atom numeric value that -will be assigned to that atom. IDs can be listed in any order. -

    -

    IMPORTANT NOTE: Every time a set of per-atom lines is read, the value -for all atoms is first set to 0.0. Thus values for atoms whose ID -does not appear in the set, will remain 0.0. -

    -

    For the python style a Python function name is provided. This needs -to match a function name specified in a python command -which returns a value to this variable as defined by its return -keyword. For exampe these two commands would be self-consistent: -

    -
    variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py 
-
    -

    The two commands can appear in either order so long as both are -specified before the Python function is invoked for the first time. -

    -

    Each time the variable is evaluated, the associated Python function is -invoked, and the value it returns is also returned by the variable. -Since the Python function can use other LAMMPS variables as input, or -query interal LAMMPS quantities to perform its computation, this means -the variable can return a different value each time it is evaluated. -

    -

    The type of value stored in the variable is determined by the format -keyword of the python command. It can be an integer -(i), floating point (f), or string (s) value. As mentioned above, if -it is a numeric value (integer or floating point), then the -python-style variable can be used in place of an equal-style variable -anywhere in an input script, e.g. as an argument to another command -that allows for equal-style variables. -

    -
    - -

    For the equal and atom styles, a single string is specified which -represents a formula that will be evaluated afresh each time the -variable is used. If you want spaces in the string, enclose it in -double quotes so the parser will treat it as a single argument. For -equal style variables the formula computes a scalar quantity, which -becomes the value of the variable whenever it is evaluated. For -atom style variables the formula computes one quantity for each -atom whenever it is evaluated. -

    -

    Note that equal and atom variables can produce different values at -different stages of the input script or at different times during a -run. For example, if an equal variable is used in a fix -print command, different values could be printed each -timestep it was invoked. If you want a variable to be evaluated -immediately, so that the result is stored by the variable instead of -the string, see the section below on "Immediate Evaluation of -Variables". -

    -

    The next command cannot be used with equal or atom style -variables, since there is only one string. -

    -

    The formula for an equal or atom variable can contain a variety -of quantities. The syntax for each kind of quantity is simple, but -multiple quantities can be nested and combined in various ways to -build up formulas of arbitrary complexity. For example, this is a -valid (though strange) variable formula: -

    -
    variable x equal "pe + c_MyTemp / vol^(1/3)" 
-
    -

    Specifically, an formula can contain numbers, thermo keywords, math -operators, math functions, group functions, region functions, atom -values, atom vectors, compute references, fix references, and -references to other variables. -

    -
    - - - - - - - - - - - - - -
    Number 0.2, 100, 1.0e20, -15.4, etc
    Constant PI, version, on, off, true, false, yes, no
    Thermo keywords vol, pe, ebond, etc
    Math operators (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
    Math operators (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x
    Math functions sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
    Group functions count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)
    Region functions count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)
    Special functions sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
    Atom values id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
    Atom vectors id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
    Compute references c_ID, c_ID[i], c_ID[i][j]
    Fix references f_ID, f_ID[i], f_ID[i][j]
    Other variables v_name, v_name[i] -
    - -
    - -

    Most of the formula elements produce a scalar value. A few produce a -per-atom vector of values. These are the atom vectors, compute -references that represent a per-atom vector, fix references that -represent a per-atom vector, and variables that are atom-style -variables. Math functions that operate on scalar values produce a -scalar value; math function that operate on per-atom vectors do so -element-by-element and produce a per-atom vector. -

    -

    A formula for equal-style variables cannot use any formula element -that produces a per-atom vector. A formula for an atom-style variable -can use formula elements that produce either a scalar value or a -per-atom vector. Atom-style variables are evaluated by other commands -that define a group on which they operate, e.g. a -dump or compute or fix command. -When they invoke the atom-style variable, only atoms in the group are -inlcuded in the formula evaluation. The variable evaluates to 0.0 for -atoms not in the group. -

    -

    Constants are set at compile time and cannot be changed. PI will -return the number 3.14159265358979323846; on, true or yes will -return 1.0; off, false or no will return 0.0; version will -return a numeric version code of the current LAMMPS version (e.g. -version 2 Sep 2015 will return the number 20150902). The corresponding -value for newer versions of LAMMPS will be larger, for older versions -of LAMMPS will be smaller. This can be used to have input scripts -adapt automatically to LAMMPS versions, when non-backwards compatible -syntax changes are introduced. Here is an illustrative example (which -will not work, since the version has been introduced more recently): -

    -
    if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes" 
-
    -

    The thermo keywords allowed in a formula are those defined by the -thermo_style custom command. Thermo keywords that -require a compute to calculate their values such as -"temp" or "press", use computes stored and invoked by the -thermo_style command. This means that you can -only use those keywords in a variable if the style you are using with -the thermo_style command (and the thermo keywords associated with that -style) also define and use the needed compute. Note that some thermo -keywords use a compute indirectly to calculate their value (e.g. the -enthalpy keyword uses temp, pe, and pressure). If a variable is -evaluated directly in an input script (not during a run), then the -values accessed by the thermo keyword must be current. See the -discussion below about "Variable Accuracy". -

    -
    - -

    Math Operators -

    -

    Math operators are written in the usual way, where the "x" and "y" in -the examples can themselves be arbitrarily complex formulas, as in the -examples above. In this syntax, "x" and "y" can be scalar values or -per-atom vectors. For example, "ke/natoms" is the division of two -scalars, where "vy+vz" is the element-by-element sum of two per-atom -vectors of y and z velocities. -

    -

    Operators are evaluated left to right and have the usual C-style -precedence: unary minus and unary logical NOT operator "!" have the -highest precedence, exponentiation "^" is next; multiplication and -division and the modulo operator "%" are next; addition and -subtraction are next; the 4 relational operators "<", "<=", ">", and -">=" are next; the two remaining relational operators "==" and "!=" -are next; then the logical AND operator "&&"; and finally the logical -OR operator "||" has the lowest precedence. Parenthesis can be used -to group one or more portions of a formula and/or enforce a different -order of evaluation than what would occur with the default precedence. -

    -

    IMPORTANT NOTE: Because a unary minus is higher precedence than -exponentiation, the formula "-2^2" will evaluate to 4, not -4. This -convention is compatible with some programming languages, but not -others. As mentioned, this behavior can be easily overridden with -parenthesis; the formula "-(2^2)" will evaluate to -4. -

    -

    The 6 relational operators return either a 1.0 or 0.0 depending on -whether the relationship between x and y is TRUE or FALSE. For -example the expression x<10.0 in an atom-style variable formula will -return 1.0 for all atoms whose x-coordinate is less than 10.0, and 0.0 -for the others. The logical AND operator will return 1.0 if both its -arguments are non-zero, else it returns 0.0. The logical OR operator -will return 1.0 if either of its arguments is non-zero, else it -returns 0.0. The logical NOT operator returns 1.0 if its argument is -0.0, else it returns 0.0. -

    -

    These relational and logical operators can be used as a masking or -selection operation in a formula. For example, the number of atoms -whose properties satifsy one or more criteria could be calculated by -taking the returned per-atom vector of ones and zeroes and passing it -to the compute reduce command. -

    -
    - -

    Math Functions -

    -

    Math functions are specified as keywords followed by one or more -parenthesized arguments "x", "y", "z", each of which can themselves be -arbitrarily complex formulas. In this syntax, the arguments can -represent scalar values or per-atom vectors. In the latter case, the -math operation is performed on each element of the vector. For -example, "sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)" -yields a per-atom vector with each element being the sqrt() of the -product of one atom's y and z coordinates. -

    -

    Most of the math functions perform obvious operations. The ln() is -the natural log; log() is the base 10 log. -

    -

    The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z = -seed. It generates a uniform random number between lo and hi. The -normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and -z = seed. It generates a Gaussian variate centered on mu with -variance sigma^2. In both cases the seed is used the first time the -internal random number generator is invoked, to initialize it. For -equal-style variables, every processor uses the same seed so that they -each generate the same sequence of random numbers. For atom-style -variables, a unique seed is created for each processor, based on the -specified seed. This effectively generates a different random number -for each atom being looped over in the atom-style variable. -

    -

    IMPORTANT NOTE: Internally, there is just one random number generator -for all equal-style variables and one for all atom-style variables. -If you define multiple variables (of each style) which use the -random() or normal() math functions, then the internal random number -generators will only be initialized once, which means only one of the -specified seeds will determine the sequence of generated random -numbers. -

    -

    The ceil(), floor(), and round() functions are those in the C math -library. Ceil() is the smallest integer not less than its argument. -Floor() if the largest integer not greater than its argument. Round() -is the nearest integer to its argument. -

    -

    The ramp(x,y) function uses the current timestep to generate a value -linearly intepolated between the specified x,y values over the course -of a run, according to this formula: -

    -
    value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) 
-
    -

    The run begins on startstep and ends on stopstep. Startstep and -stopstep can span multiple runs, using the start and stop keywords -of the run command. See the run command for -details of how to do this. -

    -

    The stagger(x,y) function uses the current timestep to generate a new -timestep. X,y > 0 and x > y are required. The generated timesteps -increase in a staggered fashion, as the sequence -x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next -timestep in the sequence is returned. Thus if stagger(1000,100) is -used in a variable by the dump_modify every -command, it will generate the sequence of output timesteps: -

    -
    100,1000,1100,2000,2100,3000,etc 
-
    -

    The logfreq(x,y,z) function uses the current timestep to generate a -new timestep. X,y,z > 0 and y < z are required. The generated -timesteps are on a base-z logarithmic scale, starting with x, and the -y value is how many of the z-1 possible timesteps within one -logarithmic interval are generated. I.e. the timesteps follow the -sequence x,2x,3x,...y*x,x*z,2x*z,3x*z,...y*x*z,x*z^2,2x*z^2,etc. For -any current timestep, the next timestep in the sequence is returned. -Thus if logfreq(100,4,10) is used in a variable by the dump_modify -every command, it will generate this sequence of -output timesteps: -

    -
    100,200,300,400,1000,2000,3000,4000,10000,20000,etc 
-
    -

    The logfreq2(x,y,z) function is similar to logfreq, except a single -logarithmic interval is divided into y equally-spaced timesteps and -all of them are output. Y < z is not required. Thus, if -logfreq2(100,18,10) is used in a variable by the dump_modify -every command, then the interval between 100 and -1000 is divided as 900/18 = 50 steps, and it will generate the -sequence of output timesteps: -

    -
    100,150,200,...950,1000,1500,2000,...9500,10000,15000,etc 
-
    -

    The stride(x,y,z) function uses the current timestep to generate a new -timestep. X,y >= 0 and z > 0 and x <= y are required. The generated -timesteps increase in increments of z, from x to y, i.e. it generates -the sequece x,x+z,x+2z,...,y. If y-x is not a multiple of z, then -similar to the way a for loop operates, the last value will be one -that does not exceed y. For any current timestep, the next timestep -in the sequence is returned. Thus if stride(1000,2000,100) is used -in a variable by the dump_modify every command, it -will generate the sequence of output timesteps: -

    -
    1000,1100,1200, ... ,1900,2000 
-
    -

    The stride2(x,y,z,a,b,c) function is similar to the stride() function -except it generates two sets of strided timesteps, one at a coarser -level and one at a finer level. Thus it is useful for debugging, -e.g. to produce output every timestep at the point in simulation when -a problem occurs. X,y >= 0 and z > 0 and x <= y are required, as are -a,b >= 0 and c > 0 and a < b. Also, a >= x and b <= y are required so -that the second stride is inside the first. The generated timesteps -increase in increments of z, starting at x, until a is reached. At -that point the timestep increases in increments of c, from a to b, -then after b, increments by z are resumed until y is reached. For any -current timestep, the next timestep in the sequence is returned. Thus -if stride(1000,2000,100,1350,1360,1) is used in a variable by the -dump_modify every command, it will generate the -sequence of output timesteps: -

    -
    1000,1100,1200,1300,1350,1351,1352, ... 1359,1360,1400,1500, ... ,2000 
-
    -

    The vdisplace(x,y) function takes 2 arguments: x = value0 and y = -velocity, and uses the elapsed time to change the value by a linear -displacement due to the applied velocity over the course of a run, -according to this formula: -

    -
    value = value0 + velocity*(timestep-startstep)*dt 
-
    -

    where dt = the timestep size. -

    -

    The run begins on startstep. Startstep can span multiple runs, using -the start keyword of the run command. See the -run command for details of how to do this. Note that the -thermo_style keyword elaplong = -timestep-startstep. -

    -

    The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments: -x = value0, y = amplitude, z = period. They use the elapsed time to -oscillate the value by a sin() or cos() function over the course of a -run, according to one of these formulas, where omega = 2 PI / period: -

    -
    value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
-value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt)) 
-
    -

    where dt = the timestep size. -

    -

    The run begins on startstep. Startstep can span multiple runs, using -the start keyword of the run command. See the -run command for details of how to do this. Note that the -thermo_style keyword elaplong = -timestep-startstep. -

    -
    - -

    Group and Region Functions -

    -

    Group functions are specified as keywords followed by one or two -parenthesized arguments. The first argument ID is the group-ID. -The dim argument, if it exists, is x or y or z. The dir -argument, if it exists, is xmin, xmax, ymin, ymax, zmin, or -zmax. The dimdim argument, if it exists, is xx or yy or zz -or xy or yz or xz. -

    -

    The group function count() is the number of atoms in the group. The -group functions mass() and charge() are the total mass and charge of -the group. Xcm() and vcm() return components of the position and -velocity of the center of mass of the group. Fcm() returns a -component of the total force on the group of atoms. Bound() returns -the min/max of a particular coordinate for all atoms in the group. -Gyration() computes the radius-of-gyration of the group of atoms. See -the compute gyration command for a definition -of the formula. Angmom() returns components of the angular momentum -of the group of atoms around its center of mass. Torque() returns -components of the torque on the group of atoms around its center of -mass, based on current forces on the atoms. Inertia() returns one of -6 components of the symmetric inertia tensor of the group of atoms -around its center of mass, ordered as Ixx,Iyy,Izz,Ixy,Iyz,Ixz. -Omega() returns components of the angular velocity of the group of -atoms around its center of mass. -

    -

    Region functions are specified exactly the same way as group functions -except they take an extra final argument IDR which is the region ID. -The function is computed for all atoms that are in both the group and -the region. If the group is "all", then the only criteria for atom -inclusion is that it be in the region. -

    -
    - -

    Special Functions -

    -

    Special functions take specific kinds of arguments, meaning their -arguments cannot be formulas themselves. -

    -

    The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions -each take 1 argument which is of the form "c_ID" or "c_ID[N]" or -"f_ID" or "f_ID[N]". The first two are computes and the second two -are fixes; the ID in the reference should be replaced by the ID of a -compute or fix defined elsewhere in the input script. The compute or -fix must produce either a global vector or array. If it produces a -global vector, then the notation without "[N]" should be used. If -it produces a global array, then the notation with "[N]" should be -used, when N is an integer, to specify which column of the global -array is being referenced. -

    -

    These functions operate on the global vector of inputs and reduce it -to a single scalar value. This is analagous to the operation of the -compute reduce command, which invokes the same -functions on per-atom and local vectors. -

    -

    The sum() function calculates the sum of all the vector elements. The -min() and max() functions find the minimum and maximum element -respectively. The ave() function is the same as sum() except that it -divides the result by the length of the vector. -

    -

    The trap() function is the same as sum() except the first and last -elements are multiplied by a weighting factor of 1/2 when performing -the sum. This effectively implements an integration via the -trapezoidal rule on the global vector of data. I.e. consider a set of -points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2), -..., (N,VN), where the Vi are the values in the global vector of -length N. The integral from 1 to N of these points is trap(). When -appropriately normalized by the timestep size, this function is useful -for calculating integrals of time-series data, like that generated by -the fix ave/correlate command. -

    -

    The slope() function uses linear regression to fit a line to the set -of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2), -..., (N,VN), where the Vi are the values in the global vector of -length N. The returned value is the slope of the line. If the line -has a single point or is vertical, it returns 1.0e20. -

    -

    The gmask(x) function takes 1 argument which is a group ID. It -can only be used in atom-style variables. It returns a 1 for -atoms that are in the group, and a 0 for atoms that are not. -

    -

    The rmask(x) function takes 1 argument which is a region ID. It can -only be used in atom-style variables. It returns a 1 for atoms that -are in the geometric region, and a 0 for atoms that are not. -

    -

    The grmask(x,y) function takes 2 arguments. The first is a group ID, -and the second is a region ID. It can only be used in atom-style -variables. It returns a 1 for atoms that are in both the group and -region, and a 0 for atoms that are not in both. -

    -

    The next(x) function takes 1 argument which is a variable ID (not -"v_foo", just "foo"). It must be for a file-style or atomfile-style -variable. Each time the next() function is invoked (i.e. each time -the equal-style or atom-style variable is evaluated), the following -steps occur. -

    -

    For file-style variables, the current string value stored by the -file-style variable is converted to a numeric value and returned by -the function. And the next string value in the file is read and -stored. Note that if the line previously read from the file was not a -numeric string, then it will typically evaluate to 0.0, which is -likely not what you want. -

    -

    For atomfile-style variables, the current per-atom values stored by -the atomfile-style variable are returned by the function. And the -next set of per-atom values in the file is read and stored. -

    -

    Since file-style and atomfile-style variables read and store the first -line of the file or first set of per-atoms values when they are -defined in the input script, these are the value(s) that will be -returned the first time the next() function is invoked. If next() is -invoked more times than there are lines or sets of lines in the file, -the variable is deleted, similar to how the next command -operates. -

    -
    - -

    Feature Functions -

    -

    Feature functions allow to probe the running LAMMPS executable for -whether specific features are either active, defined, or available. -The functions take two arguments, a category and a corresponding -argument. The arguments are strings thus cannot be formulas -themselves (only $-style immediate variable expansion is possible). -Return value is either 1.0 or 0.0 depending on whether the function -evaluates to true or false, respectively. -

    -

    The is_active() function allows to query for active settings which -are grouped by categories. Currently supported categories and -arguments are: -

    -
    • package (argument = cuda or gpu or intel or kokkos or omp) -
    • newton (argument = pair or bond or any) -
    • pair (argument = single or respa or manybody or tail or shift) -
    • comm_style (argument = brick or tiled) -
    • min_style (argument = any of the compiled in minimizer styles) -
    • run_style (argument = any of the compiled in run styles) -
    • atom_style (argument = any of the compiled in atom styles) -
    • pair_style (argument = any of the compiled in pair styles) -
    • bond_style (argument = any of the compiled in bond styles) -
    • angle_style (argument = any of the compiled in angle styles) -
    • dihedral_style (argument = any of the compiled in dihedral styles) -
    • improper_style (argument = any of the compiled in improper styles) -
    • kspace_style (argument = any of the compiled in kspace styles) -
    -

    Most of the settings are self-explanatory, the single argument in the -pair category allows to check whether a pair style supports a -Pair::single() function as needed by compute group/group and others -features or LAMMPS, respa allows to check whether the inner/middle/outer -mode of r-RESPA is supported. In the various style categories, -the checking is also done using suffix flags, if available and enabled. -

    -

    Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP). -

    -
    pair_style lj/cut/coul/long 14.0
-if $(is_active(package,gpu)) then "suffix off"
-kspace_style pppm 
-
    -

    Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step -

    -
    timestep $(2.0*(1.0+*is_active(pair,respa))
-if $(is_active(pair,respa)) then "run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2  improper 1 pair 2 kspace 3" 
-
    -

    The is_defined() function allows to query categories like compute, -dump, fix, group, region, and variable whether an entry -with the provided name or id is defined. -

    -

    The is_available() function allows to query whether a specific -optional feature is available, i.e. compiled in. This currently -works for the following categories: command, compute, fix, -and pair_style. For all categories except command also appending -active suffixes is tried before reporting failure. -

    -
    - -

    Atom Values and Vectors -

    -

    Atom values take an integer argument I from 1 to N, where I is the -atom-ID, e.g. x[243], which means use the x coordinate of the atom -with ID = 243. Or they can take a variable name, specified as v_name, -where name is the name of the variable, like x[v_myIndex]. The -variable can be of any style except atom or atom-file variables. The -variable is evaluated and the result is expected to be numeric and is -cast to an integer (i.e. 3.4 becomes 3), to use an an index, which -must be a value from 1 to N. Note that a "formula" cannot be used as -the argument between the brackets, e.g. x[243+10] or -x[v_myIndex+1] are not allowed. To do this a single variable can be -defined that contains the needed formula. -

    -

    Note that the 0 < atom-ID <= N, where N is the largest atom ID -in the system. If an ID is specified for an atom that does not -currently exist, then the generated value is 0.0. -

    -

    Atom vectors generate one value per atom, so that a reference like -"vx" means the x-component of each atom's velocity will be used when -evaluating the variable. -

    -

    The meaning of the different atom values and vectors is mostly -self-explanatory. Mol refers to the molecule ID of an atom, and is -only defined if an atom_style is being used that -defines molecule IDs. -

    -

    Note that many other atom attributes can be used as inputs to a -variable by using the compute -property/atom command and then specifying -a quantity from that compute. -

    -
    - -

    Compute References -

    -

    Compute references access quantities calculated by a -compute. The ID in the reference should be replaced by -the ID of a compute defined elsewhere in the input script. As -discussed in the doc page for the compute command, -computes can produce global, per-atom, or local values. Only global -and per-atom values can be used in a variable. Computes can also -produce a scalar, vector, or array. An equal-style variable can only -use scalar values, which means a global scalar, or an element of a -global or per-atom vector or array. Atom-style variables can use the -same scalar values. They can also use per-atom vector values. A -vector value can be a per-atom vector itself, or a column of an -per-atom array. See the doc pages for individual computes to see what -kind of values they produce. -

    -

    Examples of different kinds of compute references are as follows. -There is no ambiguity as to what a reference means, since computes -only produce global or per-atom quantities, never both. -

    -
    - - -
    c_ID global scalar, or per-atom vector
    c_ID[I] Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array
    c_ID[I][J] I,J element of global array, or atom I's Jth value in per-atom array -
    - -

    For I and J, integers can be specified or a variable name, specified -as v_name, where name is the name of the variable. The rules for this -syntax are the same as for the "Atom Values and Vectors" discussion -above. -

    -

    If a variable containing a compute is evaluated directly in an input -script (not during a run), then the values accessed by the compute -must be current. See the discussion below about "Variable Accuracy". -

    -
    - -

    Fix References -

    -

    Fix references access quantities calculated by a fix. -The ID in the reference should be replaced by the ID of a fix defined -elsewhere in the input script. As discussed in the doc page for the -fix command, fixes can produce global, per-atom, or local -values. Only global and per-atom values can be used in a variable. -Fixes can also produce a scalar, vector, or array. An equal-style -variable can only use scalar values, which means a global scalar, or -an element of a global or per-atom vector or array. Atom-style -variables can use the same scalar values. They can also use per-atom -vector values. A vector value can be a per-atom vector itself, or a -column of an per-atom array. See the doc pages for individual fixes -to see what kind of values they produce. -

    -

    The different kinds of fix references are exactly the same as the -compute references listed in the above table, where "c_" is replaced -by "f_". Again, there is no ambiguity as to what a reference means, -since fixes only produce global or per-atom quantities, never both. -

    -
    - - -
    f_ID global scalar, or per-atom vector
    f_ID[I] Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array
    f_ID[I][J] I,J element of global array, or atom I's Jth value in per-atom array -
    - -

    For I and J, integers can be specified or a variable name, specified -as v_name, where name is the name of the variable. The rules for this -syntax are the same as for the "Atom Values and Vectors" discussion -above. -

    -

    If a variable containing a fix is evaluated directly in an input -script (not during a run), then the values accessed by the fix should -be current. See the discussion below about "Variable Accuracy". -

    -

    Note that some fixes only generate quantities on certain timesteps. -If a variable attempts to access the fix on non-allowed timesteps, an -error is generated. For example, the fix ave/time -command may only generate averaged quantities every 100 steps. See -the doc pages for individual fix commands for details. -

    -
    - -

    Variable References -

    -

    Variable references access quantities stored or calculated by other -variables, which will cause those variables to be evaluated. The name -in the reference should be replaced by the name of a variable defined -elsewhere in the input script. -

    -

    As discussed on this doc page, equal-style variables generate a global -scalar numeric value; atom-style and atomfile-style variables generate -a per-atom vector of numeric values; all other variables store a -string. The formula for an equal-style variable can use any style of -variable except an atom-style or atomfile-style (unless only a single -value from the variable is accessed via a subscript). If a -string-storing variable is used, the string is converted to a numeric -value. Note that this will typically produce a 0.0 if the string is -not a numeric string, which is likely not what you want. The formula -for an atom-style variable can use any style of variable, including -other atom-style or atomfile-style variables. -

    -

    Examples of different kinds of variable references are as follows. -There is no ambiguity as to what a reference means, since variables -produce only a global scalar or a per-atom vector, never both. -

    -
    - -
    v_name scalar, or per-atom vector
    v_name[I] atom I's value in per-atom vector -
    - -

    For I, an integer can be specified or a variable name, specified as -v_name, where name is the name of the variable. The rules for this -syntax are the same as for the "Atom Values and Vectors" discussion -above. -

    -
    - -

    Immediate Evaluation of Variables: -

    -

    If you want an equal-style variable to be evaluated immediately, it -may be the case that you do not need to define a variable at all. See -Section 3.2 of the manual, which -describes the use of "immediate" variables in an input script, -specified as $(formula) with parenthesis, where the formula has the -same syntax as equal-style variables described on this page. This -effectively evaluates a formula immediately without using the variable -command to define a named variable. -

    -

    More generally, there is a difference between referencing a variable -with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v_" -(e.g. v_x or v_abc). The former can be used in any input script -command, including a variable command. The input script parser -evaluates the reference variable immediately and substitutes its value -into the command. As explained in Section commands -3.2 for "Parsing rules", you can also use -un-named "immediate" variables for this purpose. For example, a -string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script -command evaluates the string between the parenthesis as an equal-style -variable formula. -

    -

    Referencing a variable with a leading "v_" is an optional or required -kind of argument for some commands (e.g. the fix -ave/spatial or dump custom or -thermo_style commands) if you wish it to evaluate -a variable periodically during a run. It can also be used in a -variable formula if you wish to reference a second variable. The -second variable will be evaluated whenever the first variable is -evaluated. -

    -

    As an example, suppose you use this command in your input script to -define the variable "v" as -

    -
    variable v equal vol 
-
    -

    before a run where the simulation box size changes. You might think -this will assign the initial volume to the variable "v". That is not -the case. Rather it assigns a formula which evaluates the volume -(using the thermo_style keyword "vol") to the variable "v". If you -use the variable "v" in some other command like fix -ave/time then the current volume of the box will be -evaluated continuously during the run. -

    -

    If you want to store the initial volume of the system, you can do it -this way: -

    -
    variable v equal vol
-variable v0 equal $v 
-
    -

    The second command will force "v" to be evaluated (yielding the -initial volume) and assign that value to the variable "v0". Thus the -command -

    -
    thermo_style custom step v_v v_v0 
-
    -

    would print out both the current and initial volume periodically -during the run. -

    -

    Note that it is a mistake to enclose a variable formula in double -quotes if it contains variables preceeded by $ signs. For example, -

    -
    variable vratio equal "${vfinal}/${v0}" 
-
    -

    This is because the quotes prevent variable substitution (see this -section on parsing input script -commands), and thus an error will occur when the formula for "vratio" -is evaluated later. -

    -
    - -

    Variable Accuracy: -

    -

    Obviously, LAMMPS attempts to evaluate variables containing formulas -(equal and atom style variables) accurately whenever the -evaluation is performed. Depending on what is included in the -formula, this may require invoking a compute, either -directly or indirectly via a thermo keyword, or accessing a value -previously calculated by a compute, or accessing a value calculated -and stored by a fix. If the compute is one that calculates -the pressure or energy of the system, then these quantities need to be -tallied during the evaluation of the interatomic potentials (pair, -bond, etc) on timesteps that the variable will need the values. -

    -

    LAMMPS keeps track of all of this during a run or energy -minimization. An error will be generated if you -attempt to evaluate a variable on timesteps when it cannot produce -accurate values. For example, if a thermo_style -custom command prints a variable which accesses -values stored by a fix ave/time command and the -timesteps on which thermo output is generated are not multiples of the -averaging frequency used in the fix command, then an error will occur. -

    -

    An input script can also request variables be evaluated before or -after or in between runs, e.g. by including them in a -print command. In this case, if a compute is needed to -evaluate a variable (either directly or indirectly), LAMMPS will not -invoke the compute, but it will use a value previously calculated by -the compute, and can do this only if it was invoked on the current -timestep. Fixes will always provide a quantity needed by a variable, -but the quantity may or may not be current. This leads to one of -three kinds of behavior: -

    -

    (1) The variable may be evaluated accurately. If it contains -references to a compute or fix, and these values were calculated on -the last timestep of a preceeding run, then they will be accessed and -used by the variable and the result will be accurate. -

    -

    (2) LAMMPS may not be able to evaluate the variable and will generate -an error message stating so. For example, if the variable requires a -quantity from a compute that has not been invoked on -the current timestep, LAMMPS will generate an error. This means, for -example, that such a variable cannot be evaluated before the first run -has occurred. Likewise, in between runs, a variable containing a -compute cannot be evaluated unless the compute was invoked on the last -timestep of the preceding run, e.g. by thermodynamic output. -

    -

    One way to get around this problem is to perform a 0-timestep run -before using the variable. For example, these commands -

    -
    variable t equal temp
-print "Initial temperature = $t"
-run 1000 
-
    -

    will generate an error if the run is the first run specified in the -input script, because generating a value for the "t" variable requires -a compute for calculating the temperature to be invoked. -

    -

    However, this sequence of commands would be fine: -

    -
    run 0
-variable t equal temp
-print "Initial temperature = $t"
-run 1000 
-
    -

    The 0-timestep run initializes and invokes various computes, including -the one for temperature, so that the value it stores is current and -can be accessed by the variable "t" after the run has completed. Note -that a 0-timestep run does not alter the state of the system, so it -does not change the input state for the 1000-timestep run that -follows. Also note that the 0-timestep run must actually use and -invoke the compute in question (e.g. via thermo or -dump output) in order for it to enable the compute to be -used in a variable after the run. Thus if you are trying to print a -variable that uses a compute you have defined, you can insure it is -invoked on the last timestep of the preceding run by including it in -thermodynamic output. -

    -

    Unlike computes, fixes will never generate an error if -their values are accessed by a variable in between runs. They always -return some value to the variable. However, the value may not be what -you expect if the fix has not yet calculated the quantity of interest -or it is not current. For example, the fix indent -command stores the force on the indenter. But this is not computed -until a run is performed. Thus if a variable attempts to print this -value before the first run, zeroes will be output. Again, performing -a 0-timestep run before printing the variable has the desired effect. -

    -

    (3) The variable may be evaluated incorrectly and LAMMPS may have no -way to detect this has occurred. Consider the following sequence of -commands: -

    -
    pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-variable e equal pe
-print "Final potential energy = $e" 
-
    -

    The first run is performed using one setting for the pairwise -potential defined by the pair_style and -pair_coeff commands. The potential energy is -evaluated on the final timestep and stored by the compute -pe compute (this is done by the -thermo_style command). Then a pair coefficient is -changed, altering the potential energy of the system. When the -potential energy is printed via the "e" variable, LAMMPS will use the -potential energy value stored by the compute pe -compute, thinking it is current. There are many other commands which -could alter the state of the system between runs, causing a variable -to evaluate incorrectly. -

    -

    The solution to this issue is the same as for case (2) above, namely -perform a 0-timestep run before the variable is evaluated to insure -the system is up-to-date. For example, this sequence of commands -would print a potential energy that reflected the changed pairwise -coefficient: -

    -
    pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-run 0
-variable e equal pe
-print "Final potential energy = $e" 
-
    -
    - -

    Restrictions: -

    -

    Indexing any formula element by global atom ID, such as an atom value, -requires the atom style to use a global mapping in order to look up -the vector indices. By default, only atom styles with molecular -information create global maps. The atom_modify -map command can override the default. -

    -

    All universe- and uloop-style variables defined in an input script -must have the same number of values. -

    -

    Related commands: -

    -

    next, jump, include, -temper, fix print, print -

    -

    Default: none -

    - diff --git a/doc/doc2/velocity.html b/doc/doc2/velocity.html deleted file mode 100644 index 5e06774da6..0000000000 --- a/doc/doc2/velocity.html +++ /dev/null @@ -1,270 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    velocity command -

    -

    Syntax: -

    -
    velocity group-ID style args keyword value ... 
-
    -
    • group-ID = ID of group of atoms whose velocity will be changed - -
    • style = create or set or scale or ramp or zero - -
        create args = temp seed
-    temp = temperature value (temperature units)
-    seed = random # seed (positive integer)
-  set args = vx vy vz
-    vx,vy,vz = velocity value or NULL (velocity units)
-    any of vx,vy,vz van be a variable (see below)
-  scale arg = temp
-    temp = temperature value (temperature units)
-  ramp args = vdim vlo vhi dim clo chi
-    vdim = vx or vy or vz
-    vlo,vhi = lower and upper velocity value (velocity units)
-    dim = x or y or z
-    clo,chi = lower and upper coordinate bound (distance units)
-  zero arg = linear or angular
-    linear = zero the linear momentum
-    angular = zero the angular momentum 
-
      -
    • zero or more keyword/value pairs may be appended - -
    • keyword = dist or sum or mom or rot or temp or bias or loop or units - -
        dist value = uniform or gaussian
-  sum value = no or yes
-  mom value = no or yes 
-  rot value = no or yes 
-  temp value = temperature compute ID
-  bias value = no or yes 
-  loop value = all or local or geom
-  rigid value = fix-ID
-    fix-ID = ID of rigid body fix
-  units value = box or lattice 
-
      - -
    -

    Examples: -

    -
    velocity all create 300.0 4928459 rot yes dist gaussian
-velocity border set NULL 4.0 v_vz sum yes units box
-velocity flow scale 300.0
-velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
-velocity all zero linear 
-
    -

    Description: -

    -

    Set or change the velocities of a group of atoms in one of several -styles. For each style, there are required arguments and optional -keyword/value parameters. Not all options are used by each style. -Each option has a default as listed below. -

    -

    The create style generates an ensemble of velocities using a random -number generator with the specified seed as the specified temperature. -

    -

    The set style sets the velocities of all atoms in the group to the -specified values. If any component is specified as NULL, then it is -not set. Any of the vx,vy,vz velocity components can be specified as -an equal-style or atom-style variable. If the value -is a variable, it should be specified as v_name, where name is the -variable name. In this case, the variable will be evaluated, and its -value used to determine the velocity component. Note that if a -variable is used, the velocity it calculates must be in box units, not -lattice units; see the discussion of the units keyword below. -

    -

    Equal-style variables can specify formulas with various mathematical -functions, and include thermo_style command -keywords for the simulation box parameters or other parameters. -

    -

    Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent -velocity field. -

    -

    The scale style computes the current temperature of the group of -atoms and then rescales the velocities to the specified temperature. -

    -

    The ramp style is similar to that used by the compute -temp/ramp command. Velocities ramped -uniformly from vlo to vhi are applied to dimension vx, or vy, or vz. -The value assigned to a particular atom depends on its relative -coordinate value (in dim) from clo to chi. For the example above, an -atom with y-coordinate of 10 (1/4 of the way from 5 to 25), would be -assigned a x-velocity of 1.25 (1/4 of the way from 0.0 to 5.0). Atoms -outside the coordinate bounds (less than 5 or greater than 25 in this -case), are assigned velocities equal to vlo or vhi (0.0 or 5.0 in this -case). -

    -

    The zero style adjusts the velocities of the group of atoms so that -the aggregate linear or angular momentum is zero. No other changes -are made to the velocities of the atoms. If the rigid option is -specified (see below), then the zeroing is performed on individual -rigid bodies, as defined by the fix rigid or fix -rigid/small commands. In other words, zero linear -will set the linear momentum of each rigid body to zero, and zero -angular will set the angular momentum of each rigid body to zero. -This is done by adjusting the velocities of the atoms in each rigid -body. -

    -

    All temperatures specified in the velocity command are in temperature -units; see the units command. The units of velocities and -coordinates depend on whether the units keyword is set to box or -lattice, as discussed below. -

    -

    For all styles, no atoms are assigned z-component velocities if the -simulation is 2d; see the dimension command. -

    -
    - -

    The keyword/value options are used in the following ways by the -various styles. -

    -

    The dist keyword is used by create. The ensemble of generated -velocities can be a uniform distribution from some minimum to -maximum value, scaled to produce the requested temperature. Or it can -be a gaussian distribution with a mean of 0.0 and a sigma scaled to -produce the requested temperature. -

    -

    The sum keyword is used by all styles, except zero. The new -velocities will be added to the existing ones if sum = yes, or will -replace them if sum = no. -

    -

    The mom and rot keywords are used by create. If mom = yes, the -linear momentum of the newly created ensemble of velocities is zeroed; -if rot = yes, the angular momentum is zeroed. -

    -

    *line -

    -

    If specified, the temp keyword is used by create and scale to -specify a compute that calculates temperature in a -desired way, e.g. by first subtracting out a velocity bias, as -discussed in Section howto 16 of the doc -pages. If this keyword is not specified, create and scale -calculate temperature using a compute that is defined internally as -follows: -

    -
    compute velocity_temp group-ID temp 
-
    -

    where group-ID is the same ID used in the velocity command. i.e. the -group of atoms whose velocity is being altered. This compute is -deleted when the velocity command is finished. See the compute -temp command for details. If the calculated -temperature should have degrees-of-freedom removed due to fix -constraints (e.g. SHAKE or rigid-body constraints), then the -appropriate fix command must be specified before the velocity command -is issued. -

    -

    The bias keyword with a yes setting is used by create and -scale, but only if the temp keyword is also used to specify a -compute that calculates temperature in a desired way. -If the temperature compute also calculates a velocity bias, the the -bias is subtracted from atom velocities before the create and -scale operations are performed. After the operations, the bias is -added back to the atom velocities. See Section howto -16 of the doc pages for more discussion -of temperature computes with biases. Note that the velocity bias is -only applied to atoms in the temperature compute specified with the -temp keyword. -

    -

    As an example, assume atoms are currently streaming in a flow -direction (which could be separately initialized with the ramp -style), and you wish to initialize their thermal velocity to a desired -temperature. In this context thermal velocity means the per-particle -velocity that remains when the streaming velocity is subtracted. This -can be done using the create style with the temp keyword -specifying the ID of a compute temp/ramp or -compute temp/profile command, and the -bias keyword set to a yes value. -

    -
    - -

    The loop keyword is used by create in the following ways. -

    -

    If loop = all, then each processor loops over all atoms in the -simulation to create velocities, but only stores velocities for atoms -it owns. This can be a slow loop for a large simulation. If atoms -were read from a data file, the velocity assigned to a particular atom -will be the same, independent of how many processors are being used. -This will not be the case if atoms were created using the -create_atoms command, since atom IDs will likely -be assigned to atoms differently. -

    -

    If loop = local, then each processor loops over only its atoms to -produce velocities. The random number seed is adjusted to give a -different set of velocities on each processor. This is a fast loop, -but the velocity assigned to a particular atom will depend on which -processor owns it. Thus the results will always be different when a -simulation is run on a different number of processors. -

    -

    If loop = geom, then each processor loops over only its atoms. For -each atom a unique random number seed is created, based on the atom's -xyz coordinates. A velocity is generated using that seed. This is a -fast loop and the velocity assigned to a particular atom will be the -same, independent of how many processors are used. However, the set -of generated velocities may be more correlated than if the all or -local keywords are used. -

    -

    Note that the loop geom keyword will not necessarily assign -identical velocities for two simulations run on different machines. -This is because the computations based on xyz coordinates are -sensitive to tiny differences in the double-precision value for a -coordinate as stored on a particular machine. -

    -
    - -

    The rigid keyword only has meaning when used with the zero style. -It allows specification of a fix-ID for one of the rigid-body -fix variants which defines a set of rigid bodies. The -zeroing of linear or angular momentum is then performed for each rigid -body defined by the fix, as described above. -

    -

    The units keyword is used by set and ramp. If units = box, -the velocities and coordinates specified in the velocity command are -in the standard units described by the units command -(e.g. Angstroms/fmsec for real units). If units = lattice, velocities -are in units of lattice spacings per time (e.g. spacings/fmsec) and -coordinates are in lattice spacings. The lattice -command must have been previously used to define the lattice spacing. -

    -
    - -

    Restrictions: -

    -

    Assigning a temperature via the create style to a system with rigid -bodies or SHAKE constraints may not -have the desired outcome for two reasons. First, the velocity command -can be invoked before all of the relevant fixes are created and -initialized and the number of adjusted degrees of freedom (DOFs) is -known. Thus it is not possible to compute the target temperature -correctly. Second, the assigned velocities may be partially canceled -when constraints are first enforced, leading to a different -temperature than desired. A workaround for this is to perform a run -0 command, which insures all DOFs are accounted for -properly, and then rescale the temperature to the desired value before -performing a simulation. For example: -

    -
    velocity all create 300.0 12345
-run 0                             # temperature may not be 300K
-velocity all scale 300.0          # now it should be 
-
    -

    Related commands: -

    -

    fix rigid, fix shake, -lattice -

    -

    Default: -

    -

    The keyword defaults are dist = uniform, sum = no, mom = yes, rot = -no, bias = no, loop = all, and units = lattice. The temp and rigid -keywords are not defined by default. -

    - diff --git a/doc/doc2/write_data.html b/doc/doc2/write_data.html deleted file mode 100644 index 426b0a2068..0000000000 --- a/doc/doc2/write_data.html +++ /dev/null @@ -1,131 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    write_data command -

    -

    Syntax: -

    -
    write_data file keyword value ... 
-
    -
    • file = name of data file to write out - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = pair or nocoeff - -
        nocoeff = do not write out force field info
-  pair value = ii or ij
-    ii = write one line of pair coefficient info per atom type
-    ij = write one line of pair coefficient info per IJ atom type pair 
-
      - -
    -

    Examples: -

    -
    write_data data.polymer
-write_data data.* 
-
    -

    Description: -

    -

    Write a data file in text format of the current state of the -simulation. Data files can be read by the read data -command to begin a simulation. The read_data command -also describes their format. -

    -

    Similar to dump files, the data filename can contain a "*" -wild-card character. The "*" is replaced with the current timestep -value. -

    -

    IMPORTANT NOTE: The write-data command is not yet fully implemented in -two respects. First, most pair styles do not yet write their -coefficient information into the data file. This means you will need -to specify that information in your input script that reads the data -file, via the pair_coeff command. Second, a few of -the atom styles (body, ellipsoid, line, tri) that -store auxiliary "bonus" information about aspherical particles, do not -yet write the bonus info into the data file. Both these -functionalities will be added to the write_data command later. -

    -

    Because a data file is in text format, if you use a data file written -out by this command to restart a simulation, the initial state of the -new run will be slightly different than the final state of the old run -(when the file was written) which was represented internally by LAMMPS -in binary format. A new simulation which reads the data file will -thus typically diverge from a simulation that continued in the -original input script. -

    -

    If you want to do more exact restarts, using binary files, see the -restart, write_restart, and -read_restart commands. You can also convert -binary restart files to text data files, after a simulation has run, -using the -r command-line switch. -

    -

    IMPORTANT NOTE: Only limited information about a simulation is stored -in a data file. For example, no information about atom -groups and fixes are stored. Binary restart -files store more information. -

    -

    Bond interactions (angle, etc) that have been turned off by the fix -shake or delete_bonds command will -be written to a data file as if they are turned on. This means they -will need to be turned off again in a new run after the data file is -read. -

    -

    Bonds that are broken (e.g. by a bond-breaking potential) are not -written to the data file. Thus these bonds will not exist when the -data file is read. -

    -
    - -

    The nocoeff keyword requests that no force field parameters should -be written to the data file. This can be very helpful, if one wants -to make significant changes to the force field or if the parameters -are read in separately anyway, e.g. from an include file. -

    -

    The pair keyword lets you specify in what format the pair -coefficient information is written into the data file. If the value -is specified as ii, then one line per atom type is written, to -specify the coefficients for each of the I=J interactions. This means -that no cross-interactions for I != J will be specified in the data -file and the pair style will apply its mixing rule, as documented on -individual pair_style doc pages. Of course this -behavior can be overridden in the input script after reading the data -file, by specifying additional pair_coeff commands -for any desired I,J pairs. -

    -

    If the value is specified as ij, then one line of coefficients is -written for all I,J pairs where I <= J. These coefficients will -include any specific settings made in the input script up to that -point. The presence of these I != J coefficients in the data file -will effectively turn off the default mixing rule for the pair style. -Again, the coefficient values in the data file can can be overridden -in the input script after reading the data file, by specifying -additional pair_coeff commands for any desired I,J -pairs. -

    -
    - -

    Restrictions: -

    -

    This command requires inter-processor communication to migrate atoms -before the data file is written. This means that your system must be -ready to perform a simulation before using this command (force fields -setup, atom masses initialized, etc). -

    -

    Related commands: -

    -

    read_data, write_restart -

    -

    Default: -

    -

    The option defaults are pair = ii. -

    - diff --git a/doc/doc2/write_dump.html b/doc/doc2/write_dump.html deleted file mode 100644 index 79dc858e56..0000000000 --- a/doc/doc2/write_dump.html +++ /dev/null @@ -1,101 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    write_dump command -

    -

    Syntax: -

    -
    write_dump group-ID style file dump-args modify dump_modify-args 
-
    -
    • group-ID = ID of the group of atoms to be dumped - -
    • style = any of the supported dump styles - -
    • file = name of file to write dump info to - -
    • dump-args = any additional args needed for a particular dump style - -
    • modify = all args after this keyword are passed to dump_modify (optional) - -
    • dump-modify-args = args for dump_modify (optional) -
    -

    Examples: -

    -
    write_dump all atom dump.atom
-write_dump subgroup atom dump.run.bin
-write_dump all custom dump.myforce.* id type x y vx fx
-write_dump flow custom dump.%.myforce id type c_myF[3] v_ke modify sort id
-write_dump all xyz system.xyz modify sort id elements O H 
-write_dump all image snap*.jpg type type size 960 960 modify backcolor white
-write_dump all image snap*.jpg element element &
-   bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &
-   modify backcolor white element C C O H N C C C O H H S O H 
-
    -

    Description: -

    -

    Dump a single snapshot of atom quantities to one or more files for the -current state of the system. This is a one-time immediate operation, -in contrast to the dump command which will will set up a -dump style to write out snapshots periodically during a running -simulation. -

    -

    The syntax for this command is mostly identical to that of the -dump and dump_modify commands as if -they were concatenated together, with the following exceptions: There -is no need for a dump ID or dump frequency and the keyword modify is -added. The latter is so that the full range of -dump_modify options can be specified for the single -snapshot, just as they can be for multiple snapshots. The modify -keyword separates the arguments that would normally be passed to the -dump command from those that would be given the dump_modify. Both -support optional arguments and thus LAMMPS needs to be able to cleanly -separate the two sets of args. -

    -

    Note that if the specified filename uses wildcard characters "*" or -"%", as supported by the dump commmand, they will operate -in the same fashion to create the new filename(s). Normally, dump -image files require a filename with a "*" character -for the timestep. That is not the case for the write_dump command; no -wildcard "*" character is necessary. -

    -
    - -

    Restrictions: -

    -

    All restrictions for the dump and -dump_modify commands apply to this command as well, -with the exception of the dump image filename not -requiring a wildcard "*" character, as noted above. -

    -

    Since dumps are normally written during a run or energy -minimization, the simulation has to be ready to run -before this command can be used. Similarly, if the dump requires -information from a compute, fix, or variable, the information needs to -have been calculated for the current timestep (e.g. by a prior run), -else LAMMPS will generate an error message. -

    -

    For example, it is not possible to dump per-atom energy with this -command before a run has been performed, since no energies and forces -have yet been calculated. See the variable doc page -sectinn on Variable Accuracy for more information on this topic. -

    -

    Related commands: -

    -

    dump, dump image, -dump_modify -

    -

    Default: -

    -

    The defaults are listed on the doc pages for the dump and -dump image and dump_modify -commands. -

    - diff --git a/doc/doc2/write_restart.html b/doc/doc2/write_restart.html deleted file mode 100644 index 8da34fb33c..0000000000 --- a/doc/doc2/write_restart.html +++ /dev/null @@ -1,130 +0,0 @@ - -
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
    - - - - - - -
    - -

    write_restart command -

    -

    Syntax: -

    -
    write_restart file keyword value ... 
-
    -
    • file = name of file to write restart information to - -
    • zero or more keyword/value pairs may be appended - -
    • keyword = fileper or nfile - -
        fileper arg = Np
-    Np = write one file for every this many processors
-  nfile arg = Nf
-    Nf = write this many files, one from each of Nf processors 
-
      - -
    -

    Examples: -

    -
    write_restart restart.equil
-write_restart restart.equil.mpiio
-write_restart poly.%.* nfile 10 
-
    -

    Description: -

    -

    Write a binary restart file of the current state of the simulation. -

    -

    During a long simulation, the restart command is -typically used to output restart files periodically. The -write_restart command is useful after a minimization or whenever you -wish to write out a single current restart file. -

    -

    Similar to dump files, the restart filename can contain -two wild-card characters. If a "*" appears in the filename, it is -replaced with the current timestep value. If a "%" character appears -in the filename, then one file is written by each processor and the -"%" character is replaced with the processor ID from 0 to P-1. An -additional file with the "%" replaced by "base" is also written, which -contains global information. For example, the files written for -filename restart.% would be restart.base, restart.0, restart.1, ... -restart.P-1. This creates smaller files and can be a fast mode of -output and subsequent input on parallel machines that support parallel -I/O. The optional fileper and nfile keywords discussed below can -alter the number of files written. -

    -

    The restart file can also be written in parallel as one large binary -file via the MPI-IO library, which is part of the MPI standard for -versions 2.0 and above. Using MPI-IO requires two steps. First, -build LAMMPS with its MPIIO package installed, e.g. -

    -
    make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform 
-
    -

    Second, use a restart filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO dump files, a particular restart file must be both -written and read using MPI-IO. -

    -

    Restart files can be read by a read_restart -command to restart a simulation from a particular state. Because the -file is binary (to enable exact restarts), it may not be readable on -another machine. In this case, you can use the -r command-line -switch to convert a restart file to a data -file. -

    -

    IMPORTANT NOTE: Although the purpose of restart files is to enable -restarting a simulation from where it left off, not all information -about a simulation is stored in the file. For example, the list of -fixes that were specified during the initial run is not stored, which -means the new input script must specify any fixes you want to use. -Even when restart information is stored in the file, as it is for some -fixes, commands may need to be re-specified in the new input script, -in order to re-use that information. Details are usually given in -the documentation of the respective command. Also, see the -read_restart command for general information -about what is stored in a restart file. -

    -
    - -

    The optional nfile or fileper keywords can be used in conjunction -with the "%" wildcard character in the specified restart file name. -As explained above, the "%" character causes the restart file to be -written in pieces, one piece for each of P processors. By default P = -the number of processors the simulation is running on. The nfile or -fileper keyword can be used to set P to a smaller value, which can -be more efficient when running on a large number of processors. -

    -

    The nfile keyword sets P to the specified Nf value. For example, if -Nf = 4, and the simulation is running on 100 processors, 4 files will -be written, by processors 0,25,50,75. Each will collect information -from itself and the next 24 processors and write it to a restart file. -

    -

    For the fileper keyword, the specified value of Np means write one -file for every Np processors. For example, if Np = 4, every 4th -processor (0,4,8,12,etc) will collect information from itself and the -next 3 processors and write it to a restart file. -

    -
    - -

    Restrictions: -

    -

    This command requires inter-processor communication to migrate atoms -before the restart file is written. This means that your system must -be ready to perform a simulation before using this command (force -fields setup, atom masses initialized, etc). -

    -

    To write and read restart files in parallel with MPI-IO, the MPIIO -package must be installed. -

    -

    Related commands: -

    -

    restart, read_restart, -write_data -

    -

    Default: none -

    -

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